geWorkbench

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==Tutorial data files==
The file [[Media:Bcell-100.zip|Bcell-100.zip]] contains the file Bcell-100.exp, which is a geWorkbench data matrix format file containing 100 Bcell experiments using Affymetrix  U95-Av2 chips.  It contains the same data as the file "webmatrix2.exp" which has been used in the tutorials previously.  The array groups have been given more descriptive names. The data has been processed using the Affymetrix MAS5 normalization routine.  It comes from the lab of Dr. Ricardo Dalla-Favera at the Institute for Cancer Research at Columbia University.  The 100 arrays represent B-cell experiments drawn from a variety of conditions, including cancerous and normal, germinal center and non-germinal center.


[[Media:Bcell-100_log2.zip|Bcell-100_log2.zip]] is the BCell-100 data normalized with the Threshold Normalizer, with the minimum value set to 1.0, and then log2 transformed.


The file [[Media:Tutorial_data.zip|Tutorial_data.zip]] (3.586 MB) contains data files in several different formats useful for the tutorials or just trying out geWorkbench.  It contains the following files:

*'''cardiogenomics.med.harvard.edu/''' -Contains 10 individual MAS5/GCOS format data files.
*'''webmatrix2_quantile_log2_dev1.2_mv0.exp''' -A geWorkbench "exp" format matrix file containing filtered, normalized data.  This data originally derives from the file "webmatrix.exp", but one group of columns has been rearranged so that each condition (phenotype) is kept in one block (webmatrix2.exp).
* '''NM_024426-Wilms.fasta''' -A Genbank nucleotide seqeuence file.
* '''NP_077744-Wilms.fasta''' -A Genbank protein seqeuence file.
* '''H1H5_HistoneDB_NHGRI.fasta''' -Contains H1 and H5 histone sequences from the NHGRI.
* '''cluster_tree_total_pearsons_84_markers.csv''' - Contains a list of 84 markers derived from hierarchical clustering of webmatrix2.
* '''640f84ClusterPearsonsSeqs.fasta''' - Contains FASTA sequences for 64 of the 84 markers in the list above.
* '''cluster_tree_total_pearsons_64of84_markers.csv''' -Contains the marker set for the 64 sequences in the above set.

The following are from older examples being phased out.
* '''ClusterTree38_Sequences.fasta''' -Contains sequences derived from hierarchical clustering (old example).
* '''cluster_tree_12markers.csv''' -Contains a list of markers derived from hierarchical clustering (old example).

==More about Bcell-100.exp==
Among the different B-cell lines represented in Bcell-100.exp are the following, with their abbreviations as used in the dataset:

Cancerous
# CLL/P-CLL - B cell chronic lymphocytic leukemia (P indicates purified, otherwise not)
# BL - Burkitt lymphoma
# DLCD/DLCL - purified DLBCL 
# FL - follicular lymphoma
# HCL - hairy cell leukemia
# PEL - primary effusion lymphoma
# D - DLBCL

where DLBCL is diffuse large B cell lymphoma

Non-cancerous
# CB - centroblasts
# CC - centrocytes
# M - memory B cells
# N - naive B cells

==About the cardiogenomics microarray dataset==

These example MAS5 format data files were obtained from the following site at Harvard University:

http://cardiogenomics.med.harvard.edu/project-detail?project_id=229

A number of MAS5 format data files are available there.

The specific project is the "Belgium Dataset of Aortic Stenosis, Congestive Cardiomyopathy and Normal LV Function", and the data is downloadable from:

http://cardiogenomics.med.harvard.edu/groups/proj1/pages/download_Hs-belgium.html

An abstract describing the study that produced them is also available, at:

http://cardiogenomics.med.harvard.edu/groups/proj2/pages/Hs-belgium_home.html