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Old 07-17-2014, 11:13 AM   #82
crazyhottommy
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Location: Gainesville

Join Date: Apr 2012
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Quote:
Originally Posted by bigmw View Post
GAGE and other methods (GSEA etc) require all genes included. This way GAGE test gene perturbations within pathways against the background of all genes. You selected a list of differentially expressed gene first, it is expected that you donít any pathways standing out in that perforeground, right? Including all genes instead of a selected list of genes give you a major advantages: you included all your data in the analysis, which is usually more powerful. In addition, you donít need some more or less arbitrary q-/p-value cutoff.

Otherwise, you code seem to work fine. You may want to check the DESeq section and the native workflow on the demo code:
http://www.bioconductor.org/packages...eqWorkflow.pdf
I did try using all the genes, but still no pathways are selected....Maybe that's just the nature of my data?
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