User:Rfriedman
Functionality Comments
Rich, add functionality comments and new feature suggestions here.
One quick inital suggestion. geWorkbench should be able to import files in the following GCG formats: sequence, mutiple sequence, and rsf.
2006
(3/23/06) A more robust couterpart of k-means clustering with statistical estimates for micorarray analysis is described in the following papers:
3/30/06 (answer: noted - no change for now) I don't like the slider to change arrays in the microarray widow. The identity of an array is a fixed, not a variable quantity. I suggest that a pull-down window for this would be better.
4/7/06 (answer: feature request 1844) I suggest asking "are you sure" when a user asks to remove a project.
4/26/06 (answer - already implemented for remote file download and all analyses) It would be very helpful if the workbench could display an hourglass, or a watch, or a sundial or something, when it ia loading or working - for example when it is loading micorarray files from a remote database.
5/25/06. (answer - fixed) I just installed Version 1.03. In the Windows menu it says version geWorkbench 1.0 and on top of the geWorkbench GUI its says geWorkbench 1.0. I suggest that
all labels give the full workbench version.
5/25/06 The two tutorial sets should be included in the download automatially.
5/25/06 (answer - that would be nice - if we had some way of knowing...no action for now.) I would like to ammend my recommendation of 4/26/06 to inlcude an estimate of the time a task will take, so that people may use it more easily.
5/25/06 (answer - if you can think of a better name, we can consider it!) When I spoke to the group, Ken had stated that the intensities in the microarray viewer did not correspond to an image of the chip. In which case the phrase "microarray viewer" is misleading. In fact I am not sure to what the intensities an spacing in microarray viewer corresponds.
5/25/06 (answer - already changed to "show arrays")I think that "Get bioassays" is a poor command on 2 grounds: 1. I am not used to "bioassays" being used in place of "arrays" or "array data". 2. We are obatining a list, rather than loading the bioassays into the program. What I think we eman then is "list arrays".
(answer - the datatype must be explicitly chosen) Additionally, it is not clear what format the arrays are being loaded (Cel, normalized probeset intensities, etc).
5/25/06 (answer - already done) Some indication that a work is in progress should be given while the arrays are being loaded.
5/25/06 (answer - caArray now provides access to a staging instance as well as a training instance. geWorkbench does not upload data to remote sources) I suggest that a dummy new source be made available to the users to learn how to access a remote source and I suggest that instructions for posting a remote source be made available. Doing these things will increase the ease with which users can use the workbench in collaborative projects.
5/30/06 The terms "marker" and "phenotypes" are not optimal. In the microarray world we use "probsets" (affymetrix) or "probes" (glass-slides) instead of "markers". "Arrays" is much more informative than "phenotypes" because there can be several arrays for a phenotype, or arrays can represent different patients rather than a phenotype, or because arrays can correspont to points in a time series. Also, you might want to reserve "phenotype" for instantiations that have precise defintions in a controlled vocabulary.
5/31/06 (answer - now uses array name. The items mentioned can be searched in the Markers component.) With respect to the tabular microarray view. There is also a "probe number" for affy chips (1,2,3. ..) based upon its position in a sort. It would be useful to have a colum for that. It would also be useful to have seperate, searchable columns for the following 3 items: 1. Probe id. 2. Gene name. 3. Gene defintion.
(If it sounds as if I am thinking of Excel here - I am).
5/31/06. (answer - feature request 1845) I strongly recommend that there be a way to reverse filtering, by a global undo command or some other means, so that the user may try different filters.
6/14/06 (answer - now using forums, but they are not and for now cannot be part of the NCICB GForge download process) Inclusion in the announcments mailing list should be made an integral part of teh downloading process.
6/14/06 (answer: feature request 1846) The "expression threshold filter" instructions should be clearer. stating "Filer values inside range" is ambiguous in that it is not clear if those values are left after filtering or removed by filtering (I believe that the later is the case). I suggest the language be changed to "remove values inside range". or "flter-out values inside range".
6/29/06 (answer - can't follow what is meant) I recently did some Hierarchical Clustering using Cluster 3.0. Instead of simply filtering by absolute M value, its also enables the user to retain genes that are larger than a given m value in a user-specifiable
- of experiments. It also offers the following options:
1. % present >= of chips (this only works if you use present/absent thresholds rather than statistical noise. 2. SD gene vector >=X to remove genes with insufficient variability. 3. Max-Min >= another variability filter.
I can see why someone might want to use 2 or 3.
7/17/06 Tabular microrarray format - The column widths on the tabular microarray format should be sufficient to accommodate the whole title of the chip.
7/17/06 (answer - this is really up to the user. We can mention this in the tutorial) The color mosaic only makes sense if the data already has a log2 or other variance-stabilization transformation. As is, an unsuspecting user can look at real values at this can be confusing. Furthermore, heatmaps make the most sense for log ratio comparisons versus a standard.
8/8/06 (answer - it is just a viewer of data one already has. We could perhaps add new "Save as" options to the Project folders component for microarry data, for example, tab-delimited rather than just "exp" format. But in this case, the array sets would be lost.... feature requeset 1849) The tabular micorarray viewer should be savable as an Excel spreadsheet. all tables should be savable as an excel spreadsheets.
8/10/06 A linear or spline fit to the reference line in the scatterplot would be helpful.
8/11/06 (answer - entered as addition to feature request 1845). A good filter feature would be to give the user an option of accepting or rejecting the filtering based upon the number that survived the filtering prior to acceptance. Also, there should be the option of blowing up the heatmap. In general the functionality of cluster 3.0 (written by our own Michiel de Hoon) and JavaTreeview should be reproduce for clustering.
8/14/06 (answer - entered as feature request 1850) A word about t-tests. It is very common in the microarray field for experimentalists to not give sufficient numbers of replicates to get good statistics. The word in the statistical community is to use some variant of a Bayesian t-test which pools variances of similar sample sizes to take into compensate for small smaple size. This started with Cyber-T, but the 3 most used and validated ones are: 1. LIMMA (LInear Models for Microarray Analsysis) from Gordon Smyth based on earlier work by Terry Speed and Ingrid 2. SAM (Significance Analsysis for Micorarrays) by Tibrishani and coworkers. 3. The method included in BRBArray tools, by Simon, Radamacher, and cowrkers.
I am told that LIMMA and SAM give similar results to one another and that BRBArrayTools gives somewhat different results to the two former programs, but not necessarily inferior results.
GeneSpring and GeneTraffic also have their own versions of this method. My anecdotal experiene is that GeneTraffic does not match the results from LIMMA.
I recommend that some version(s) of the Bayesian method be included in geWorkbench. Both LIMMA and SAM are available as part of Bioconductor and therefore can be ported to geWorkbench as part of a of a general Bioconductor port.
8/14/06 (answer - a long-standing wish - entered as feature request 1851) i strongly recommed that the benjamini-Hochberg False discovery rate correction be offered as an option. In fact all of the options in the current version of AffyLmGUI would find use.
8/14/06 I suggest that the heat map rather than the volcano plot be the default display on the t-test output.
8/15/06 (answer - component discontinued) With respect to the multiple t-test, an obvious improvement, alluded to in the functionality write-up is to take into account multiple comparisons. The most basic way to do this is to add terms corresponding to the variance of all of the smaple studied in the denominator of the expression for t. An expresion for this appears in the powerpoint presentation that I gave to the geWorkbench development group. This correct is different and more fundamental than additional multiple comparison corrections Bonferroni, Benjamini-Hochberg etc. Indeed doing Benjamin-Hochberg corrections for multiple tests (probesets, i.e. "markers) and multiple phenotypes simultaneously has not been implemented by the microarray statistical community to my knowledge. So I wouldn't worry about it for geWorkbench. However LIMMA, SAM, and BRBarrayTools each has its own version of correction at the level of the t-test, and I suggest that at least the first two be implemented in geWorkbench.
I realize that the above paragraph might be rather cryptic. I am available to discuss the considerations involved with the developemnt team.
9/12/06 (answer - there is an outstanding feature request already entered for this) It is important that geWorkbench be able to import micoarray data in the 2 formats used by Entrez (GEO) (The Entrez Gene expression Omnibus databse). please see the Entrez site for format information.
9/12/06 (answer - geWorkbench now comes with proper Java version included by default) I have had anecdotal experience that if the latest version of Java is installed after geWorkbench is installed there is a problem and geworkbench has to be uninstalled and then reinsatlled to work. Xiaoqing says that this shouldn;t be the case, but I just thought I would let you know what had apparently happened.
9/13/06 (answer - interesting idea but not part of our current mission. This really belongs more with a database system and indeed caArray may support this in the future) I believe that the Workbench's utility woulf be greatly enhanced if it containded menus for submission of sequences to GenBank and Microarray data to GEO. This is especially important in the latter case where the burden of MIAME compliance is considerable. Furthermore, the time for users to specify their MIAME info is when they first read the data into the Workbench, so that the task becomes spread over and not a burden at the very end when the user has to upload into GEO in order for the manuscript to be cleared for publication. The Workbench should remind the user frequently of unspecified and unnotated files.
9/28/06 (answer - we know) A much larger assortment of chip-types should be offered.
9?28/06- A general functionality need is the ability to analyze SNP-chips for loss of heterozygosity, copy number, and whole genome associations. The best package for the first 2 is dChip. I am just learning about whle genome association analysis so that I cannot make a recommendation at this time, but expect to be able to soon. We can talk about SNP-chips if and when you are ready to pursue them.
10/5/06 When I opeb webmatrix.exp, it immediately goes to the ARACNE module. This is confusing, because the tutorial has it go to the microarray viewer.
10/11/06 (answer - feature request 1847) I suggest that the caption accompanying: Microarray Viewer: Filtering: Missing Value Filter, be changed from "Maximum number of Missing Arrays" tp "Remove markers that are missing in [NUMBER BOX] arrays". It would be much clearer.
10/12/06 (answer: Feature request 1848) That the deviation bound is in raw score units should be mentioned
in the GUI. Perhaps, someting along the lines of "Remove markers which
vary by more than [NUMBER BOX] raw scores". A filter based on standard deviation
would also be useful.
10/16/06 (answer: Feature request 1848) I tried the deviation filter again today and am convinced that the standard deviation filter is a more rational way to deviation filtering than the absolute value of the deviation. This is because it is hard to specify a meaningful standard deviation cutoff for markers, because markers vary in absolute magnitude of mean and range so widely. The standard deviation measure on the other hand scales with magnitude of mean and upper and lower boundaries. It is a much more natural choice than absolute range.
2007
4/20/07 (answer - not compatible with how geWorkbench functions - we need to know the data type) I suggest that inthe open files menu there be an "all files option".
4/21/07 1. Put a vertical line on the left of all menu windows with arrows at the top and bottom :
/\
|
|
|
|
\/
If the user doesn't see the arrows he will know to enlarge the window. Or as Ken pointed out, when I sent him the above comment, a scroll bar.
4/25/07 At the risk of sounding picky or avisual the curved around icon doesn't immediately suggest submit to me. How about a green light with the word "Run" under it?
4/25/07 (answer - nothing we can do about it right now) The Blast ouptut does not contain the colored bars denoting similarity that appears in the Blast web-site. Ken writes "I think those are extra services provided by the NCBI Blast website itself, they are not part of the data returned using a remote query." If this problem can be overcome it would make a big difference to users who, as a group, just LOVE those colored bars.
4/27/07 (answer - it has been removed in coming release version 1.7) The Option "Columbia BLAST sever" didn't work. I got a "Connection Refursed" error message: I queried the user group. Ken replied that "The Columbia BLAST service is not currently operational. There is no fixed time for its reinstatement. The reason is that the Paracel BLAST machine that we used to provide that search capability failed and was retired. We do hope to set up an interface to our cluster to run those BLAST jobs at some point." I suggest that the option of the Columbia service be removed and not restored unless and until there is actually a service corresponding to it". In the meantime users can use the NCBI service either through the web, the geWorkbench interface, or the GCG Netblast program on Cancercenter, which is especially suitable for running many successive Blast jobs as part of scripts. I set up custom databases for Blast, fasta, and Smith-Waterman searches on cancercenter at user request.
5/01/07 (answer - removed) I have it set to BLAT. The text book that appears when the mouse is over the start icon is "Start Blast search" (not blast seach). Icon
5/01/07 (answer - removed) All of the non-blast functions (BLAT, HMM, Other Algorithms) under sequence comparison should be removed because the functionality is not available). The Columbia server option should be removed from the BLAST menu for the same reason.
5/04/07. The start (curly arrow) and stop(rectangular sign) are in different places in different menus. In pattern recognition tehy are on the top of the page. In BLAST they are at the bottom of the page. A more uniform look would be helpful.
7/12/07 1.06 SPLASH does not have a user-entered Z-value cutoff so that the user is at the mercy of the system as to how many values are displayed.
?12/07 1.06 the help pages should be searchable.
7/12/07 1.06 I suggest that there be better ways to save patterns. Either, just patterns or patterns highlighted in sequences.
7/13/07 1.06 (answer - fixed: now using caGrid services, only available are shown)I think that the Globus check box should be removed until such time that Globus is available.
7/18/07 1.06 Having "exact only" as a default checkbox in the advanced pattern discovery is not a clear way to indicate the difference between exacr patterns and the use of a matrix. I suggest that this be part of a scroll down menu in basic and "exact" match be an option along with the similarity matrices.
7/26/07 1/06I am having have had trouble reproducing the finding in the first SPLASH paper that the pattern for 209 H1 histones is
G.S...[ILMV]...[ILMV]
in using the database of 208 histones that comes in the data section I cannot get a single pattern that hits all of them. However with support =100% min tokens=4 density window=12 density tokens=4 Blosum50 similarity threshhold 2 Exact onluy count sequences
I get 3 patterns each of which contains but is larger than the one in the paper: [NDE][RK].G.S...[ILMV]...[ILMV] 1.21E+87 [NDE]..G.S...[ILMV]...[ILMV] 8.21E+42 [RK].G.S...[ILMV] 3.90E+10
7/26/07 1.06 I just realized that the Z-score cutoff was supposed to be setable, and was at some point in the past, because it appears as such in the tutorial.
7/26/07 1.06 The N(26gaps)DRY pattern did not appear on my screen from the GCPRs, perhaps
because its expected Z value from the paper was -11.13 and the top patterns had Zs ranging
from 1.96E138 to 2.34E153.
Still, conscientious perspective users will try to duplicate the results in the paper.
7/26/07 1.06 The term "count sequences" does not make a difference in how Splash runs or not and its meaning is unclear looking at the interface. I suggest that it be replaced my an option that tells one how to measure the total number of occurences rather than the percentage. indeed, the user should also be able to specify support in terms of number of sequences, not just % of sequences.
7/26/07 1.06 Splash output often comes out blank. That is to say the boxes say "loading" until I click them. is there anything that I can do on my end about this?
7/26/07 1.06 (answer - this has been fixed) In the advanced box for pattern discovery there is a scroll bar with the options:
BLOSUM50 BLOSUM100 BLOSUM150
BLOSUM 50 is a similarity matrix based upon the frequency and co-occurrence in alignments of residues in short gapless blocks obtained from aligned proteins of 50% or less sequence identity.
BLOSUM 100 is a similarity matrix based upon the frequency and co-occurrence in alignments of residues in short gapless blocks obtained from aligned proteins of 100% or less sequence identity (All proteins).
So, presumably, BLOSUM 150 is a similarity matrix based upon the frequency and co-occurrence in alignments of residues in short gapless blocks obtained from aligned proteins of 150% or less sequence identity (All proteins). If so, since the maximum possible sequence identity is 100%. how does BLOSUM150 differ from BLOSUM100?
I think there is a mistake here.
Ken subsequently verified that only BLOSUM50 works, and that the development team will either remove the others OR add capability of using real ones.
7/27/07 1.06 (answer - Splash is available as a separate download from the Califano lab website/wiki. We can suggest to the Califano lab that they provide a separate web site for SPLASH)
I suggest that SPLASH be available both as a command-line open source code ans as a web-server as well as through geWorkbench. I realize that this suggestion might seem to run contrary to the Integrative Genomics Platform philosophy but I believe that just getting a pattern out of a group of sequences should not require learning to use and install the workbench. The strength of the workbench lies not just in its separate applications, some of which, like Splash are not available elsewhere, but in its ability to combine and reuse data of different types. For example the use fo SPLASH to search a blast derived dataset. It is this kind feature that can be stressed in the workbench. I propose that making Splash available through the web and as a standalone Unix command line application would increase the demand for the workbench because people will then want to use Splash in conjunction with other tools. For MAGNet grant renewal purposes, it would be helpful to be able to list the number of citations of MAGNet tools in the literature. The availability of Splash via a command line and a web interface will increase this number of citations.
7/27/07 1.06 I suggest that Postit style explanations of parameter functions appear as the mouse scrolls over the interface.
8/2/07 1.06 Exhaustive search. I suggest that the non-functioning input features be removed an only be restored when they are functional.
10/19/07 1.06 (answer: entered as feature request 1852) Promoter. This is a good tool but it might not be state of the art. The emphasis in promoter searching has shifted to using methods of finding conserved and reducing the noise by limiting the search to conserved regions. Here are some web-sites that do this: http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/ http://burgundy.cmmt.ubc.ca/oPOSSUM/ http://bioinformatics.wustl.edu/PAP (currently not available)
Another point is that these tools search a databases of sites, not a few selected sites.
Another point is that it would be better if the program to take gene names as input and found the promoters as other programs do.
12/21/07 (answer - this has been fixed) The graph that shows the expression and relative expression of several markers is extremely useful. However,
it would be more useful if array labels, rather than just
numbers. were given on the Y-axis.
12/21/07 1.06 (answer - this has been fixed) For color mosiac the tutorial states: "The buttons Pat, Abs, and Ratio, are not currently used". I suggest that they be removed from the display until, which time, if any, their functions are restored, so as to reduce confusion".
12/24/07 1.06 When I apply the missing value filter the hourglass goes on and off. It would be nice if it were continuous.
12/26/07 1.06 Differential expression. I suggest that the method by which the Bonferroni correction is adjusted be shown in the menu.
12/26/07 1.06. (answer: entered as feature request 1853 ) The user currently has a choice of either equal variance or unequal variance t-tests. This can be distinguished by the test for equality of variances (Bartlett test).
12/16/07 1.06 (answer - this is the way the webmatrix data came to us from the lab. You can fix the data using the threshold normalizer or quantile normalization). log2 transform I got an error message: This data contains non-positve data points. This should not be with raw mas5 data.
12/26/07 1.06 (answer - this has already been fixed) In the heat map generated by hierarchical clustering markers (probesets) are labelled by their Affymetrix probeset id which is not very informative. We need a way to display the names of the genes. Otherwise, this is much less useful that cluster 3.0 and JavaTreeview which can be confgured to display both gene names and probesets and be linked to web accessible databases.
12/26/07 (answer - this is available as option "both") 1.06 The ability to simultaneously cluster probesets and phenotypes would also be useful.
12/28/07 1.06 (answer - A: we could add the gene symbol. The spelled-out gene name is already displayed. A, B and C: entered as feature request 1854 ) The marker annotation feature doesn't really improve the usability much for a number of reasons.
A. One cannot tell which clusters are worth expanding and annotating from the display based on the probesets. The process of identifying the genes in each cluster by downloading the annotation is cumbersome and will not be useful relative to Genespring.
B. The cGAP databases is far from the most generally useful database. I suggest Entrez gene. I realize that cGAP is supposed to contain links to Entrez gene, but the first few genes that I tried had no cuch links. I realize that there are funding reasons associated with using cGAP, but I am wondering if Entrez gene could be added as well.
C. The cGAP pathways, whereas they supplement KEGG pathways, are not as good. Some of them in fact are too small to be useful. I suggest that KEGG pathways be added as well.
2009
5/5/09 1.63 In trying to connect to caArray I got an error message: Error could not connect to the server. Ken tells me that this is an error on the NCI end and that we have no solution. I therefore suggest that caARRAY tab be removed from the workbench. Problems like this can potentially lead to user frustration that can discourage platform adoption.
5/5/09 1.63. [answer - could not reproduce Richard's problem, may be something about the Mac. Will add to tests for 1.7 release) Ken suggested that I try array-train.nci.nih.gov,
as a test case for remote databases, but it now requires a password.
I suggest that the “Remote database” button be removed from the general
release until it is working.
05/05/09 1.63 I greatly appreciate the ability to read Affymtrix cel file images. Reading PLM images can be more informative (I will explain and give refs if you are interested).
05/05/09 1.63 (answer - feature request 1855) Color Mosaic: The ability to switch between absolute and relative expression mode without rebooting would be useful.
05/05/09 1.63 (answer - feature request 1856) The ability to label array names (not just array groups). In the color mosiac would also be useful.
05/05/09 1.63 (answer - image snapshot (right-click menu) does work for me in the development version. lightbulb is not present). Microarray viewer - gene profile. The image snapshot and the lightbulb (view graph details with mouse move-over) don't work.
05/05/09 1.63 (answer - ??? The t-test color mosaic is already sorted by p-value) Differential expression and Microarray viewer - color mosiac. The coloring of the experiment gene/array boxes would be more useful if the change as a whole could be sorted by statistical signficance.
05/05/09 1.63 (answer - The dataset history for the node will show what was actually done. The node name indicates where the data came from, in this case the t-test component. Maybe we could make it say "t-test - permutations". Noted as feature request 1857). Differential expression. The results node is reported as a t-test, even if it is a permutation test. I suggest to change label permutation tests, Random permutations, or All permutations, depending on which option is chosen.
05/05/09 1.63 I suggest that there be separate submenus for differential expression (class comparison) clustering (class discovery) and classifiers (class prediction).
05/06/09 1.63 (answer - can you alter the bioconductor output settings to create a file we can use?) Bioconductor output gene expression files cannot be read in using the
RMAexpress output format. I get the following error message.
RMexpress output files can read in.
05/07/09 1.63 Many of the programs contain a time estimate. But not ARACNE. I suggest that ARACNE contain a time-estimate window.
05/07/09 1.63 (fixed in coming version 1.7) MINDy When I run MINDy with MYC as a hub marker. 4 mapks as modulators, and all markers as targets, and I try to get a heat map, I get an error message:
There is not enough memory to display the heatmap.
05/07/09 1.63 Classfiers. I do not get the login menu for the genepattern server, and hence cannot run classfiers. I have spoken to Ken about this problem and he is looking into it. However, I suggest that if it can't be fixed by the next version, that classifers be removed, until the problem is fixed.
05/08/09
Following is a document that I had prepared for a meeting between Andrea, Aris, Paolo, and myself to discuss geWorkbench.
Richard Friedman's notes for meeting with Andrea, Aris, and Paolo about geWorkbench. 5/8/09
From: Aris Floratos
Sent: Tuesday, April 28, 2009 1:42 PM
To: Paolo Guarnieri; Richard Friedman (SMTP)
Cc: Andrea Califano; Carolyn Williams
Subject: End-user Feedback on using geWorkbench
Rich, Paolo
Andrea has requested that we setup a meeting to go over your experience using geWorkbench so that we can collect your specific comments regarding what changes would be needed in order to make geWorkbench a tool that is on par with the other microarray analysis platforms that you are using.
Introduction
1. This series of notes is not meant to detract from the achievement of geWorkbench – but is meant to list things that geWorkbench should do in order to be competitive with other graphic user interface microarray tools. It is completely between us. 2. Limit to microarrays.( I use it in my course and work for sequence pattern-finding but not microarrays). 3. geWorkbench's main value at present is that it presents a front-end to useful applications that are unavailable elseqhere: SPLASH, ARACNe,MINDY. The purpose of this document is to show how it can be made more competitive for other kinds of applications- differential expression, etc. 4. Some comments will be desireable features that are not in competing GUI platforms and if implemented will give geWorkbench an edge over competing platforms. 5. Many of my comments are to a large extent equivalent to: Write an interface to R and Bioconductor packages.
The 5 main platforms I use are
1. Bioconductor (Command line). 2. Bioconductor GUI (LimmaGUI and AffylmGUI). 3. Cluster 3.0 and JavaTreeView 4. BRBarray Tools 5. Onto-tools
Useability
I generally find geWorkbench harder to use that the above tools. I sometimes get lost and have trouble finding my way back to the right menu. I realize that this criticism is imprecise and subjective, but if I knew where I get lost I wouldn't be lost. Perhaps I can run through some exercises with somebody to see what I mean. This problem had decreased with each new version, and over the last week as I grew used to the package, but it is still there.
3 suggestions:
1. I run through the steps in the presence of one or more development team member or with my usage videoed or screen recorded. 2. A cognitive scientist specializing in HCI such as Dave Kaufman be involved. 3. An undo button or a back button would be a help.
Data Input, quality and normalization
Affymetrix: The program should read cel files and normalize them with RMA and with GCRMA. AffylmGUI can do this. So can BRBarrayools. If an investigator has to do the normalization with a GUI in a program other than geWorkbench he will be tempted to stay in that program . (The latest implementation of GCRMA in bioconductor incorporates the correction of Andrea and co-workers. Wei-Keat suggested that I run it on FAST=FALSE. When that is done, as far as Wei-Keat and I can see, it does not introduce an artifact in hierachical clustering). Quality measures such as PLM and the Affy quality measures and boxplot should be included.
2 color spotted-arrays including Agilent: It would be advantageous if geWorkbench could read the image files of arrays with a spot-reader comparable to Spot. Most spot-reader programs including the widely-used Genepix and Agilent Feature extraction assume circular spots and has a fairly simplistic background correction. Spot does not assume circularity and has a more complex background correction.Spot does better than Genepix on benchmarks. There are no tests comparing Spot to Agilent feature extraction, but there may be similar advantages to the case with cDNA arrays.Within-array Loess, Print-tip Loess, and between chip loess should be included.
Common processed files should also be read in. These include Affy
normalized intensities in a *txt format, *.gpr files, which are used by many
spotted microarray files, Agilent *txt files, Illumina files and Kinexus
proteomic, files. Although RMAexpress files cannot be read in AffulmGUI
(Bioconductor) output text files of measurements cannot be read in. The
ability to read those files as well would be useful.
The program should also allow flexible user defined formats of input and output text files.
I don't like the slider to change arrays in the microarray widow. The identity
of an array is a categorical, not a continuous variable. I suggest that a pull-
down window for array names would be better.
The term "microarray viewer" is misleading in that it does not correspond to a chip image. I believe that its use should be further clarified in the tutorial.
I suggest asking "are you sure" when a user asks to remove a project or an output tab.
It would be helpful if the program would give an estimate of the time a task will take.
With respect to the tabular microarray view. There is also a "probe number" for affy chips (1,2,3. ..) based upon its poistion in a sort. It would be useful to have a colum for that. It would also be useful to have seperate, searchable columns for the following 3 items: 1. Probe id. 2. Gene name. 3. Gene defintion.
(If it sounds as if I am thinking of Excel here - I am).
Inclusion in the announcements mailing list should be made an integral part
of the downloading process.
In trying to connect to caArray I got an error message:
Error could not connect to the server.
Ken tells me that this is an error on the NCI end and that
we have no solution. I therefore suggest that caARRAY tab be
removed from the workbench. Problems like this can potentially
lead to user frustration that can discourage platform adoption.
Ken suggested that I try array-train.nci.nih.gov,
as a test case for remote databases, but it now requires a password.
I suggest that the "Remote database" button be removed from the general
release until it is working.
I greatly appreciate the ability to read Affymetrix cel file images. Reading PLM images can be more informative (I will explain and give refs if you are interested).
Color Mosiac: The ability to switch between absolute and relative expression mode without rebooting would be useful.
Microarray viewer - gene profile. The image snapshot and the lightbulb (view graph details with mouse move-over) don't work.
Differential expression
At present geWorkbench gives a frequentist Bayesian t-test, along with
permutation methods and a Benjamini-Hochberg false discovery rate. The small
sample sizes generally used in microarray experiments plus the large number of
multiple tests leads to many fortuitously small standard deviations, which in turn
lead to many false positives when frequentist statistics are used, even with false
discovery corrections. The preferred approach in the field is some sort of
empirical Bayesian "fudge factor" that raises the standard deviation, lowers the t-
statistic, and hence reduces the number of false positives. The 3 most popular
(free-ware) programs that do this are
1. SAM (Significance Analysis of Microarrays)
2. LIMMA (Linear Models for MicroArrays) (Bioconductor)
and
3. Random variance model (BRBArrayTools).
SAM and LIMMA generally agree well with one another. Random variance model agrees less will with SAM and LIMMA than SAM and LIMMA do with one another. I prefer LIMMA to SAM because of it doesn't have a user-defined sliding delta parameter the way SAM does. Also, LIMMA can handle arbitrary linear models and linear model contrasts.
GeneSpring and GeneTraffic often do not agree with LIMMA or SAM.
Without such a correction, geWorkbench will be less useful for the small
sample common in most microarray experiments than are the 3 methods listed
above. I therefore recommend that geWorkbench incorporate Limma, or a similar
Bayesian correction method.
The ability to handle Bayesian ANOVA would put geWorkbench on a par with BRBArrayTools and LIMMA (command line).
The ability to handle Bayesian linear models would put geWorkbench on a par with LIMMA (command line) and either on on par or surpass AffylmGUI and LIMMAGUI (the GUIs can't handle as complex linear models as the command line.
Handling of factorial experiments (2-way ANOVA etc) through a GUI would give geWorkbench an advantage over other GUI platforms.
I am happy to see that the Benjamini-Hochberg FDR has been incorporated. Recent anecdotal experience and literature suggests that it may be in some cases too stringent. Offering a choice of methods BY, Storey, and Ge would give the package an advantage. Adaptation of filtering options such as coefficient of variation in the Genefilter package in Bioconductor would be helpful.
Differential expression and Microarray viewer - color mosiac. The coloring of the experiment gene/array boxes would be more useful if the change as a whole could be sorted by statistical signficance.
Annotation, summarization, Boolean operations
I suggest that geWorkbench allow the point-and-click selection of the gene annotation fields to be incorporated in output (full gene defintion, GO category. Etc, including links to online databases). Towards this end, we may wish to configure our own database files to improve with Affy's proprietary files. The Santa Cruz Table Browser may be a help in this regard. The symatlas tissue- dependent gene expession database may be helpful in this regard.
It would also be helpful, where there are multiple probesets (or oligomers) per gene to offer user-defined options for summarizing the various probeset results into a single result for a gene. Options should include: median, mean, trimmed mean, largest absolute value, largest variance, largest coefficient of variation, and Tukey compound co-variate.
Boolean (Venn operations on genelists) should also be offered. I realize they are to some extent, but their use should be clarified.
The present output format of 1 line-per-probeset-per-Biocarta pathway is cumbersome. I suggest replacement by 1 line-per-gene including all pathways.
The tabular microarray viewer should be save-able as an Excel spreadsheet. all tables should be save-able as an excel spreadsheets.
Clustering
Some statistical measure of the validity of would be a plus. Various methods in competing packages include a method by Dudoit in Bioconductor, a method by Simon in BRBArray and a bootstrap method in TMEV (put out by TIGR). All 3 methods assess whether more than one cluster is present. Dudoit's method finds the optimum number of clusters by a k-medioids method. Simon's method finds the optimal number of clusters in framework of hierarchical clustering. The method in TMEV presents the bootstrap fraction of the different clusters.
The user set width and heights of the heatmap that has been implemented in geworkbench is a valuable innovation. If it could be supplemented by find gene and probeset search techniques. The find gene techniques should include wildcards. There should also be searching by go-categories, KEGG pathways, and Biocarta pathways.
Optimal filtering methods for clustering are often different than optimal filtering methods for differential expression. With this in mind I suggest that the following options be made available for filtering prior to hierarchical clustering (taken from cluster 3.0):
1. A% genes or probesets with absolute value ≥X 2. At least M observations with absolute value ≥Y 3. SD gene vector ≥Z to remove genes with insufficient variability. 4. Max-Min ≥W.
A good filter feature would be to give the user an option of accepting or rejecting the filtering based upon the number that survived the filtering prior to acceptance.
Also, the meaning of the heatmap depends upon the reference used and the definition of intensity. For 2 color arrays a simple definition is the red/green ratio. For one color arrays, you need to define a reference. It would be great if geWorkbench could define the reference array for each experiment array on an array-by-array basis.
Overrepresentation Analysis
Finding overrepresented Biocarta pathways in genelists would be more useful that simply listing pathways for each gene. The capability of finding overrepresented KEGG pathways and gene-ontology categories would also be useful.
Regression and time series
The ability to perform linear and non-linear regressions on gene sets, including time series would be useful. The ability to correlate genes and SNPs with phenotypes by logistic regression and pick the optimum # of model parameters by __square and/or information theoretic methods would be useful and would confer a competitive advantage over other packages.
SNPs
The ability to incorporate best practice methods of SNP calling (currently CRLLM) would be advantageous, as would the ability to perform GWAS analyses.
Copy Numbers
The ability to incorporate best practice methods of copy number locus calling (currently Aroma Affymetrix) with the best method of region determination (currently Venkat's segmentation method) with the best method of distinguishing causal from byproduct copy number variations (currently GISTIC) would be advantageous.
Classifiers
I could not get the weighted voting and N-nearest neighbor classifiers
currently available in geWorkbench working (I did not get menu to connect to the
genepattern site). However, I suggest that these classifiers be supplemented by
linear discriminant analysis and support vector methods to be competitive with
BRBArrayTools. Alex Hartemink's SMLR (Sparse matrix logistic regression
method and other methods he has developed are very effective but they are
available through a GUI which starts a cross-validation loop. Incorporation of
these methods into geWorkbench would give it a competitive advantage over
BRBArrayTools. The ability to perform "leave-X%-out" in addition to leave "leave-
n-out" cross validation would be useful.
Survival
The ability to do micorarray based survival analysis as is currently done in BRBArrayTools would be beneficial. There is a method by Tibishirani incoprporated in BRBArrayTools which is especially effective. Where BRBArrayTools falls short is in its ability to rigorously evaluate whether there is any increased effectiveness upon adding expression methods to clinical survival predictors. An p-value or information theoretic way of doing this evaluation would be a great boon to the field.
END OF LONG DOCUMENT
Tutorials Comments
Tutorials comments go here.
The initial download should come with all of the datasets in the tutorial (the cardio set was missing when I installed) OR the tutorial should show where these can be downloaded.
3/30/06: Some mention of what the micorarray viewer does should be included in the manual - i.e that it shows a raw image of the chip.
3/30/06: What it means to merge microarray files should be stated more explicitly.
4/07/06 That the chip recognition message is only shown once should be stated. Alternatively maybe it should be shown each time - but not require an okay button.
4/10/06 How to save a merged affy dataset so that one may open it again shoudl be described more clearly. The following points (courtesy of Ken) should be mentioned (and illustated).
1. The set should be saved with an exp suffix.
2. The set can be reopened with the filter set to "Affymatrix Matrix file".
4/24/06 The tutorials comments for opening a remote site are misleading. It should state: 1. Go is clicked for getting the list of micorarray experiments. 2. "Get Bioassays" is necessary for getting a list of arrays in the
experiment-not for retreival.
3. "open" will retrieve the selcted bioassays. I found this veyr hard to use and required correspondence with Kem and a visit from Xiaoqing in orfer to learn to use it.
4/26/06 I suggest that the tutorial not mention adding a new site for remote downlaod umtil such sites are commonly available. Otehrwise it just begs questions from the reader/
5/25/06 I suggest that the tutorial pages state to which version of geWorkbench they apply. This is implicit in the label of the window, that appears in the screenshot, but it should also be on the web-page that the user unloads.
5/25/06 I suggest that the tutorial pages be downlaodable as a pdf file.
5/25/06 I suggest that there be a public mailing list where users can be notified of updates.
5/25/06 I suggest to what the intensities and layout on the microarray viewer slide be discussed.
5/30/06 Designating a group of arrays a "case" causes the thumbtack to be labeled red. However, designating a group of arrays as the "control" does not change the color of the thumbtack. I suggest that the color of the thumbtack be changed to green to distinguish it from a group whose nature has not been demonstrated. Also, the designation "case" is used in clinical and epidemiological research. The corresponding term in laboratory research is "experiemnt".
6/13/06 It should be explained that the microarray viewer image is in probset order split across each row and is not an actual image of the slide.
6/14/06 Examples of each the different filter options should be given in the tutorial.
7/17/06 I believe that you are doing the person learning to use geWorkbench a disservice by showing the heat map instructions in the tutorial before you have shown log transformation (or at least am assuming that there is no log trandformation because some of the numbers are so high). Heat maps are most useful relative to a standard and hence this should be used as part of a didactic example in which a log2 ratio standard is used.
7/17/06 I suggest that the instructions in the tutorial for using the scatter plot graph be more detailed and step-by-step.
8/8/06 I suggest that the difference between a project and a workspace be spelled out.
8/10/06 I suggest the tutorial note explicitly the meaning of the buttons necessary to display the heat map in the micorarray display panel.
8/10/06 There should be some discussion as to where array/phenotype labels come from in the tutorial.
8/10/06 I suggest that there be a tutorial example to plotting the array with a subset of a few probesets.
8/10/06 An illustration of using reference line in the scatterplot would be helpful.
8/14/06 A discussion of the interpretaion of heat maps and volcano plots which wouldbe helpful. I would especially appreciate this in the case of volcano plots, because although I can read the axes, I don't really know how to interpret them. Also an example in which filtering by p-value and by fold change should also be given.
9/14/06 It would helpful if the installation instructions would specify that updates of Windows sometimes includes an earlier version of Java than 1.5 and hence should be checked. It should also state that installing geWorkbench followed by Java 1.5 does not work. It should be specifically stated that the Jave insatllation proceed the geWorkbench installation and that if by mistake, Java is installed after geWorkbench, geWorkbench should be uninstalled and then reinstalled in order to work.This cautionary is consistent with a recent ptoblem I have had and its solution.
9/28/06 A picture of selecting the chip-type should be included in the tutorial which deals with the uploading wo wed-matrix2.
10/5/06 A before-and-after picture of the microaarry viewer application of each filter type to the data and a discussion of the color codes and the reasons for applying the filtering would be helpful. This discussion should include screenshots of the table showing the affect of the filtering and the change in the number of genes.
10/11/06 TI suggest changing" Discards all markers that have missing measurements in at least N microarrays, where N is set by the user" to "keeps all markers that have missing measurements in N or fewer arrays where N is set by the user", in order to bring the tutorial into agreement with what the program actually does and what is stated in the actual GUI.
10/12/06 I suggest that an explict demo of the deviation filter be given in the tutorial.
10/16/06 I suggest that the explict demo of the deviation filter include before and after shots of the tabular microarray viewer and include both absolute and standard deviation options.
4/17/07 I suggest that the tutorails be available on the gforge site.
4/18/07 That retrieving the sequences for a list of markers requires expression data to bebe loaded into the system should be stated explicitly in the tutorial.
4/21/07 Frequent mention should be made in the tutorial that on 15" diagonal screens the user should make sure the menu (otions) window is tall enough to display all of the options and if not, raise the user should raise the Window until they are visible. Please see a complmentary note that I will write today in the tutorials window.
5/3/07 The distinction between Min Tokens and Density Tokens could be clearer. I read the paper so I think I get it, but there should be an example at this point.
5/4/07 Frequent references to the existence of the online help as supplementing the tutorial would be helful.
5/4/07 Create session menu for SPLASH: Tutorial should explicitly state that the port must be set to 80 and that any username will work and that no password is required. On my end a different port number has appeared and it dosn;t work with that.
6/8/07 Version 1.06. When I click "Taxonomy Tree" on the blast output, I don't get anything.
7/12/07 1.06 There should be clear examples as to the meaning of the 3 splash input parameters, with pointers to the variables in the paper. Also, there shoudl be more splash examples. The one given is a good first example, from a technical viewpoint but its biological interest is not meaningful to the user. An example such as the ones in the original splash paper and its sequels will exhibit the power fo the method better.
7/13/07 1.06 This comment applies more to the help pages than to the tutorial per se. The help pages link to the SPLASH pages at IBM. The SPLASH pages at IBM look funny (one long column) when lined to from the help window. furthermore, the pdf files thereby accessed don't come across. in order to read the IBM pages properly, I had to paste teh URL directly into my browser. Since some things have to be explaiend more throughly that is presently the case in the local documentation (e.g. exhaustive discovery) this linking problem presnets an obstacle to use. I suggest that the relevant portiosn of the IBM page be imported directly to the HELP pages.
7/13/07 Since Globus doesn;t work, I suggest that the discussion of it be removed from the help pages, until such time when it does work.
7/18/07 1.06 It would be helpful if the histone example from the first splash paper were to be used as an example in addiiton to the one given.
7/26/07 1.06 The help page for advanced includes the Z-acore which does not appear in the current dialog box.
7/26/07 1.06 the User Guide provides protein-based examples with a clearly labeled test set that comes with the distribution. The web-based tutorial only contains a nucleic-acid based example, which is fine as far as it goes, but which does not fully illustrate the biological power of the program. I suggest that all or part of the User Guide examples be included in the online tutorial. Itr would still be a helpfu, however, l to have the exact same test sets as in the original paper.
7/27/07 1.06 A mooment on the user guide (not tutorial). p. 50 "we will load a database and attempt to discover a common motif in at least 95% of the sequences". However, the example on p. 52 states "Support 80%".
7/27/07 1.06 In my experience a "User Guide" is a general introduction to the conventions of a software application, whereas a "Manual" is an detailed description of the operation of its packages. I think the "User Guide" is really a "Manual" albeit an incomplete one.
7/27/07 1.06 On page 52 of the tutorial, the screenshot shows the sequences displayed with the location represented as a motif. In version 1.06 this only occurs when the higher level Tab that says "sequence" is selected. This is not shown in the user guide.
7/27/07 1.06 I think that the user guide and the online tutorial should be merged. I think that the added detail in the manual really helps orient the user.
7/27/07 1.06 If I am not mistaken the default is exact match. The example in the User Guide will therefore not work as written, because you have to uncheck Exact Only to get it to work.
8/2/07 1.06 The User-Guide on "Exhaustive pattern search" is not very helpful in that it does not state what the parameters mean. Exhaustive searches are not covered in the tutorial document. The section on "exhaustive discovery" under "pattern discovery" in the online databases does not really apply to the current implmetaion in that it treats searching databases selected from a menu rather than a set of sequences loaded into the program.
8/2/07 1.06 In general the user guide should contain everything in the tutorial and the online help. Having to go to 3 differnet docuemnts (plus the IBM splash teatment plus the papers) to figure out what is goin on is a barrier to learning to use the software.
does not really apply
10/19/07 1.06 promoter. Some mention of how the JASPAR Core PSSMs are modified and how the search is done would be informative.
10/22/07 1.06 GO term enrichment. The instructions for loading the marker list in the tutorial are not clear. I loaded the list by clicking "new" under the marker sets and reache the csv file that way. This should be made clearer, step-by-step in the tutorial.
12/14/07 1.06 In the tutorial - dated 8/16/06 Under Arrays/Phenotype se there are now many more sets than are covered in the manual. I suggest that this be updated when the tutorial is revised.
12/14/07 1.06 In the tutorial - dated 3/12/07 Under Viewing microarray datasets, it shows the viewing of a *.cel file. I suggest that a sample *.cel be included in the tutorial dataset and that reading it in be demonstrated in updates of the tutorial.
12/17/07 1.06 I am using color mosaic on the Affymetrix B-cell dataset with GC B-cell and non GC B-cell selected. When I turn the intensity slide-wire some cells appear as green. I was under the impression that this data is the raw data extracted from the cel file with Mas5 without additional centering or normalization. Is this correct? If so, shouldn't all of the values be positive (red)?
12/21/07 1.06 I suggest that a screenshot of the menu that shows the saved image be shown at this point in the tutorial and explicit instructions be given. Otherwise it took me a while to realize that the image was saved.
12/26/07 1.06 Differential expression. I suggested that the tutorial screenshot be updated to replace "class" with "ultrashort designation".
12/26/07 1.06 The tutorila uses the Bonferroni correction, as an exmaple and correctly says that it is the most stringent. It is so stringent that it is generally not used in practice. In practice, the Benjamini-Hochberg FDR is most commonly used. As I have remarked in the comment on the tutorials section, it is not clear if the Benjamin-Hochberg FDR is the one meant by adjusted FDR.
12/26/07 1.06 Quantile normaization:The difference between "mean profile marker and mean microarray values is not clear".
05/05/09 1.63 I suggest that the tutorial section which deals with Remote databases be removed from general access until the remote database capability is working,
05/05/09 1.63 I suggest that the tutorial section include reading in from Rmaexpress format BUT most especially a point-by-point example of assembling an experiment file complete with data subset names.
05/05/09 1.63 Tutorial data subset 08/16/06 What geWorkbench calls "Source short" the tutorial calls "Cell line".
05/05/09 1.63 Tutorial Viewing a microarray dataset. 08/16/06 The necessity of setting the color mosiac to "relative" in the absolute display, to get a red, white, and blue map, is not mentioned until the end of the tutorial section. It should be alluded to when the red, white and blue display first appears.
05/05/09 1.63 Tutorial Viewing a microarray dataset. 08/16/06 A step-by-step guide to getting an expression profile with a few genes would be helpful.
05/05/09 1.63 Tutorial Filtering and normalizing 12/22/06 A worked example with a 2 color array such as Agilent would be helpful.
05/05/09 1.63 Tutorial Filtering and normalizing 12/22/06 A distinction should be made throughout the document as to the difference between normalizaing in the sense of getting intensities, (whether Affymetrix or 2 color) and normalizing for a heat map representing certain features.
05/05/09 1.63 Tutorial Expression value distribution 12/22/06 I would have to see a more step-by-step version this tutorial section, before I would understand the use of the freature. For example is it on probes or probsets.
05/05/09 1.63 Differential Expression 12/22/06 I suggest bringing the subset designations in the Array/Phenotype set in the file and in the tutorial into agreement.
05/05/09 1.63 Differential Expression 12/22/06 I suggest that the necessity of activating a subset before declaring it case or control be clarified.
05/05/09 1.63 Differential Expression 12/22/06 I suggest that the tutorial be updated to include the "Data log2 transformed" box on the p-value parameter menu.
05/05/09 1.63 Differential Expression and color mosiac 12/22/06 The reference state for the colors in the color mosiac here should be stated explicitly. Is it over all the genes whether their arrays are selected or not?
5/05/09 1.63 Differential Expression 12/22/06 I suggest that the section covering the multi t-test be removed from the tutorial because the multi-t-test has been removed from the package.
5/05/09 1.63 Differential Expression 12/22/06 I suggest that a section covering the ANOVA functionality of the package be added.
5/06/09 1.63 ARACNE 03/16/09 The example in the screenshoot does not correspond to the example in the text.
5/06/09 1.63 ARACNE 03/16/09 I understand that ARACNE requires a large and diverse set of relatively samples to work. I suggest that number, diversity, and purity requirements be stated so as to avoid investigators using ARACNE on datasets for which it is inapplicable,
05/07/09 1.63 ARACNE 03/16/09 The ARACNE tutorial refers to the cytoscape tutorial. There is, at present, no cytoscape tutorial in the geWorkbench tutorial.
05/06/09 1.63 ARACNE 03/16/09 I suggest that following up on cytoscape links be incorporated into the ARACNE tutorial.
05/07/09 1.63 MINDy 02/04/09 I suggest that the tutorial exercise be made more explicit, with a hub gene and a modulator file available in tutorial data be specified.
05/07/09 1.63 MINDy 02/04/09 I suggest that the tutorial exercise include the saving of the target genes.
05/07/09 1.63 Classification 05/23/07 I suggest that if the clasifier module is indeed not working, as discussed in the functionality, the classification section be removed from
the tutorial, until classification is working,
working.
