GSEA - Revision history

Smith: /* Results */

2015-02-11T15:44:56Z

‎Results

2014-01-24T20:31:56Z

‎References - GenePattern

2014-01-24T20:29:28Z

‎References - GSEA

2014-01-24T20:29:07Z

‎References

2014-01-15T18:41:43Z

‎Technical Note

2014-01-14T23:02:13Z

‎Results

2014-01-14T22:56:19Z

‎Results

2014-01-14T22:55:15Z

‎Results

2014-01-14T22:54:29Z

‎Results

2014-01-14T22:45:54Z

‎References

← Older revision		Revision as of 15:44, 11 February 2015
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	The figures shown below were generated using the BCell-100.exp data file, which is of type HG-U95Av2. The two classes selected were "non-GC B-cell" and "non-GC Tumor".		The figures shown below were generated using the BCell-100.exp data file, which is of type HG-U95Av2. The two classes selected were "non-GC B-cell" and "non-GC Tumor".

−	The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case ~~the operating system is not compatible with this (e.g.~~ 64-bit ~~Windows~~) ~~then~~ the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA, including Excel-format files. A few are depicted below.	+	The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA, including Excel-format files. A few are depicted below.

@@ Line 115: / Line 115: @@
 ==References - GenePattern==
-Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
+* Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
 ==References - GSEA==

@@ Line 125: / Line 125: @@
 ==References - GSEA==
 * Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.  Proc Natl Acad Sci U S A. 102(43):15545-50. [http://www.ncbi.nlm.nih.gov/pubmed/16199517 PubMed 16199517]
 * [http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEA/14 GSEA v14] online documentation.
 * Guide to [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Interpreting_GSEA_Results interpreting GSEA Results]

@@ Line 114: / Line 114: @@
 * When there is more than one GSEA result node, the user can switch between them.  The correct result zip files will be unpacked.  If they are being viewed in an external browser, it should be noted that the html index files share common names, i.e. are not result-node specific, although they point to result-specific files.  Refreshing an old top-level results page would then display the data from the currently selected result.
-==References==
+==References - GenePattern==
+Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
 * [http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEA/14 GSEA v14] online documentation.
 * Guide to [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Interpreting_GSEA_Results interpreting GSEA Results]

@@ Line 110: / Line 110: @@
 ==Technical Note==
-The GSEA components are found in the "gpmodule_v3_0" package in the geWorkbench component source tree.
+* The GSEA components are found in the "gpmodule_v3_0" package in the geWorkbench component source tree.
 ==References==

← Older revision		Revision as of 23:02, 14 January 2014
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	==Results==		==Results==
		+	The figures shown below were generated using the BCell-100.exp data file, which is of type HG-U95Av2. The two classes selected were "non-GC B-cell" and "non-GC Tumor".

	The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case the operating system is not compatible with this (e.g. 64-bit Windows) then the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA, including Excel-format files. A few are depicted below.		The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case the operating system is not compatible with this (e.g. 64-bit Windows) then the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA, including Excel-format files. A few are depicted below.

← Older revision		Revision as of 22:56, 14 January 2014
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	==Results==		==Results==

−	The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case the operating system is not compatible with this (e.g. 64-bit Windows) then the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA. A few are depicted below.	+	The GSEA result report is displayed either in geWorkbench, using a built-in browser, or in the case the operating system is not compatible with this (e.g. 64-bit Windows) then the user can display the result page in an external web browser window. The report contains links to the various result files generated by GSEA, including Excel-format files. A few are depicted below.

← Older revision		Revision as of 22:55, 14 January 2014
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−	The Enrichment Snapshot:	+	The Enrichment Snapshot (partial, first six graphs only):

@@ Line 90: / Line 90: @@
 ==Results==
 [[Image:GSEA_Results_Report.png]]
 [[Image:GSEA_Enrichment_Results_Snapshot.png]]