User talk:Smith - Revision history

Smith: /* Discards */

2012-11-30T18:05:14Z

‎Discards

Smith: /* Questions needing answers */

2012-11-30T18:04:06Z

‎Questions needing answers

Smith: /* Bcell MRA analysis */

2012-11-30T18:03:39Z

‎Bcell MRA analysis

Smith: /* New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0 */

2012-11-30T18:03:17Z

‎New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0

Smith: /* stuff cut out from other pages for possible later reuse: */

2012-11-30T18:03:03Z

‎stuff cut out from other pages for possible later reuse:

Smith at 19:51, 15 May 2011

2011-05-15T19:51:20Z

Smith: /* Multi t-test */

2011-05-15T19:50:57Z

‎Multi t-test

Smith: /* Removed from MINDy tutorial because in fact we do not check these parameter files in the aracne version used in mindy */

2011-05-13T23:17:03Z

‎Removed from MINDy tutorial because in fact we do not check these parameter files in the aracne version used in mindy

Smith: /* New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0 */

2011-05-12T21:09:20Z

‎New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0

Smith: /* New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0 */

2011-05-12T20:43:29Z

‎New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0

← Older revision		Revision as of 18:05, 30 November 2012
Line 731:		Line 731:
	* Selection model confusing		* Selection model confusing
	o Many objects maintaining their own internal selected data structures		o Many objects maintaining their own internal selected data structures
−
−	~~=Discards=~~
−
−	~~==View ARACNe==~~
−
−	ARACNe produces as output an adjacency matrix. This contains the MI score for each pair of expression profiles compared. The Cytoscape component can be used to visualize and further manipulate the inferred connectivity data, included selecting sets of interesting genes and returning them to the Markers component as a new set. A description of Cystoscape is located in the Cytoscape Tutorial and Help.
−
−	~~[[Image:T_ARACNE_results.png]]~~
−
−	~~==Selecting markers back into the Markers component in Cytoscape:==~~
−
−	~~Using the mouse, left click and draw a box around markers of interest in the Cytoscape display. The enclosed markers will be highlighted in yellow.~~
−
−	~~[[Image:T_ARACNE_Cytoscape_selecting_nodes.png]]~~
−
−	~~The highlighted markers will also be returned to the Markers component as follows:~~
−
−	~~1. By default, the highlighted markers are returned to the default "Selection" set.~~
−
−	~~2. Alternatively, any existing set can be "tagged" by right-clicking on it and selecting "Tag for visualization". Any markers highlighted in Cytoscape will now be returned to the "tagged" set.~~
−
−
−	~~==CDH2 - TFAP2A promoter scan results==~~
−
−
−	~~[[Image:T_Promoter_CDH2_5UTR.png]]~~
−
−	~~[[Image:T_Promoter_CDH2_5UTR-2.png]]~~
−
−	~~[[Image:T_Promoter_UCSC_24010231.png]]~~
−
−	~~[[Image:T_Promoter_UCSC_24010000.png]]~~
−
−
−
−
−	~~===Discontinued GForge-based Mailing Lists===~~
−	~~The following information on the previously used mailing lists is maintained here temporarily for reference use only:~~
−
−
−	~~{\|border="1" cellpadding="5" style="border: 1px solid lightGray"~~
−	~~!Mailing list\|\|Target Audience\|\|Description~~
−	\|-
−	\|-
−	~~\|width="150"\|geworkbench-announce@gforge.nci.nih.gov~~
−	~~\|End-users~~
−	~~\|Receive announcements about new software releases.~~
−	~~Posting is open only to the list administrator. To receive postings subscribe at http://gforge.nci.nih.gov/mailman/listinfo/geworkbench-announce.~~
−	\|-
−	\|-
−	~~\|width="150"\|[mailto:geworkbench-users@gforge.nci.nih.gov geworkbench-users@gforge.nci.nih.gov]~~
−	~~\|End-users~~
−	~~\|Post questions regarding use of geWorkbench components. Submit suggestions for improvements and requests for the addition of new functionality.~~
−	~~Posting is open only to list members. Subscribe at http://gforge.nci.nih.gov/mailman/listinfo/geworkbench-users.~~
−	\|-
−	\|-
−	~~\|width="150"\|[mailto:geworkbench-developers@gforge.nci.nih.gov geworkbench-developers@gforge.nci.nih.gov]~~
−	~~\|Developers~~
−	~~\|Post questions and issues regarding the development of geWorkbench plugins as well as suggestions for extensions to the core packages and the underlying BISON data models.~~
−	~~Posting is open only to list members. Subscribe at http://gforge.nci.nih.gov/mailman/listinfo/geworkbench-developers.~~
−	\|-
−	\|-
−	\|}

@@ Line 41: / Line 41: @@
 * The DPI tolerance is normally set between 0 and 0.15, since values larger than 0.15 yield higher false positives.
 * See the [[Tutorial_-_ARACNE|ARACNe]] tutorial page and Margolin et al. 2006 for further details on use of DPI.
 ==Retired geWorkbench tutorial pages==

← Older revision		Revision as of 18:03, 30 November 2012
Line 1:		Line 1:
−	~~==Bcell MRA analysis==~~
−	~~===Prerequisites===~~
−	# Obtain the annotation file for the HG-U95Av2 array type from the Affymetrix NetAffx website (http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu95). The name will be similar to "HG_U95Av2.na29.annot.csv", where na29 is the version number. Loading the annotation file associates gene names and other information with the Affymetrix probeset IDs (see the geWorkbench FAQ for details on obtaining these files).
−	~~# Store in your disk the following 2 files:~~
−	## [[Media:Interaction_network.txt \| Interaction_network.txt]]: describes an interaction network with 1955 nodes and 3810 edges. The file has 1955 lines (one for each node, the node name is the first entry in every line) and each line lists the edges emanating from that node. Edges are describes as tab-delimited pairs where the first member of the pair is the name of the target node and the second member is a number specifying a weight for the edge (MRA does not use the weight information but other geWorkbench components do). Node names correspond to marker ids.
−	## [[Media:Master_regulators.csv \| Master_regulators.csv]]: a list of master regulators. The marker ids in this file correspond to genes whose [http://www.geneontology.org/ Gene Ontology] annotation (under the Molecular Function category) lists them as transcription factors.
−
−
−
−
	==Multi t-test==		==Multi t-test==

← Older revision		Revision as of 18:03, 30 November 2012
Line 12:		Line 12:

	[[Multi_t_test]]		[[Multi_t_test]]
−
−	~~==New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0==~~
−
−
−
−	~~[[Image:Cytoscape_control_zoom_display_all_select.png]]~~
−
−
−
−
−
−	~~In the image below, the view has been zoomed in:~~
−	~~[[Image:Cytoscape_display_controls_v2.2.png]]~~

	==Removed from MINDy tutorial because in fact we do not check these parameter files in the aracne version used in mindy==		==Removed from MINDy tutorial because in fact we do not check these parameter files in the aracne version used in mindy==

@@ Line 723: / Line 723: @@
@@ Line 877: / Line 763: @@
      * Selection model confusing
            o Many objects maintaining their own internal selected data structures
 =Discards=

@@ Line 1: / Line 1: @@
-=Bcell MRA analysis=
+==Bcell MRA analysis==
-==Prerequisites==
+===Prerequisites===
 # Obtain the annotation file for the HG-U95Av2 array type from the Affymetrix NetAffx website (http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu95). The name will be similar to "HG_U95Av2.na29.annot.csv", where na29 is the version number. Loading the annotation file associates gene names and other information with the Affymetrix probeset IDs (see the geWorkbench FAQ for details on obtaining these files).
 # Store in your disk the following 2 files:

← Older revision		Revision as of 19:50, 15 May 2011
Line 1:		Line 1:
		+	=Bcell MRA analysis=
		+	==Prerequisites==
		+	# Obtain the annotation file for the HG-U95Av2 array type from the Affymetrix NetAffx website (http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu95). The name will be similar to "HG_U95Av2.na29.annot.csv", where na29 is the version number. Loading the annotation file associates gene names and other information with the Affymetrix probeset IDs (see the geWorkbench FAQ for details on obtaining these files).
		+	# Store in your disk the following 2 files:
		+	## [[Media:Interaction_network.txt \| Interaction_network.txt]]: describes an interaction network with 1955 nodes and 3810 edges. The file has 1955 lines (one for each node, the node name is the first entry in every line) and each line lists the edges emanating from that node. Edges are describes as tab-delimited pairs where the first member of the pair is the name of the target node and the second member is a number specifying a weight for the edge (MRA does not use the weight information but other geWorkbench components do). Node names correspond to marker ids.
		+	## [[Media:Master_regulators.csv \| Master_regulators.csv]]: a list of master regulators. The marker ids in this file correspond to genes whose [http://www.geneontology.org/ Gene Ontology] annotation (under the Molecular Function category) lists them as transcription factors.
		+
		+
		+
		+
	==Multi t-test==		==Multi t-test==

← Older revision		Revision as of 23:17, 13 May 2011
Line 35:		Line 35:

	Note that these default file names will be seen and the contents used by all versions of ARACNe, both standalone and within MINDy. So you should remove or rename these files before doing any other work with ARACNe/MINDy.		Note that these default file names will be seen and the contents used by all versions of ARACNe, both standalone and within MINDy. So you should remove or rename these files before doing any other work with ARACNe/MINDy.
		+
		+	==Removed from MINDy tutorial because DPI not used==
		+
		+	====DPI settings (Not used in MINDy)====
		+	The Data Processing Inequality (triangle inequality) can be used to remove the effects of indirect interactions, e.g. if TF1->TF2->Target, the DPI can be used to remove the indirect action of TF1 on the target. Stated another way, the DPI can be used to remove the weakest interaction of those between any three markers. Setting the DPI Tolerance is independent of whether a DPI Target List is used.
		+
		+	=====DPI Target List (Not used in MINDy)=====
		+	The DPI target list can be used to limit the ARACNE calculation to transcriptional networks. It is used to screen out spurious regulatory interaction signals of genes that are tightly coexpressed but are not in a regulatory relationship to each other, for example genes for proteins that are used to build a protein complex. The eukaryotic ribosome, for example, needs the stoichiometric expression of about 80 proteins, but those proteins are not in a regulatory relationship to each other.
		+
		+	* The specified markers will be given preferential treatment during the DPI edge-removal step. Edges originating from markers on this list will not be removed by edges originating from markers not on this list. However, for DPI calculations where all three markers are members of the list, the weakest connecting edge may still be removed.
		+
		+	* If used, it is suggested that the DPI Target List should contain all markers that are annotated as transcription factors. Signaling proteins could also be included.
		+
		+	* A comma-separated list of markers can be typed in to the text field, or it can be loaded from an external file.
		+
		+	=====DPI Tolerance (Not used in MINDy)=====
		+	The DPI tolerance specifies the degree of MI sampling error to be accepted, as with a finite sample size an exact value MI cannot be calculated.
		+	* The DPI tolerance is normally set between 0 and 0.15, since values larger than 0.15 yield higher false positives.
		+	* See the [[Tutorial_-_ARACNE\|ARACNe]] tutorial page and Margolin et al. 2006 for further details on use of DPI.

	==Questions needing answers==		==Questions needing answers==

@@ Line 7: / Line 7: @@
--[[Image:Cytoscape_control_zoom_display_all_selected_done.png]]
+[[Image:Cytoscape_control_zoom_display_all_select.png]]
--[[Image:Cytoscape_control_plus.png]]
+In the image below, the view has been zoomed in:
+[[Image:Cytoscape_display_controls_v2.2.png]]
 ==Removed from MINDy tutorial because in fact we do not check these parameter files in the aracne version used in mindy==

← Older revision		Revision as of 20:43, 12 May 2011
Line 4:		Line 4:

	==New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0==		==New Screenshots for use in the Cytoscape tutorial for geWorkbench v2.2.0==
−	~~Most of these are exact replacements for existing screenshots, just added _v2.2 to the existing names.~~	+