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Old 07-17-2014, 12:49 PM   #83
Location: Wuhan, China

Join Date: Oct 2013
Posts: 20

I very appreciate your information! Very helpful to further my understanding on the statistical background of GAGE.

Originally Posted by bigmw View Post
This is normal. Different analysis procedures give you different p-values, although you can still see lot of consistency between the them (the top hits or order of significant pathways). We expect native gage/pathview workflow to be more sensitive than the joint workflows due to the design of GAGE analysis procedure. Importantly, GAGE takes the sample size into account by default, but average fold change scores output from other tools don’t have that info.
For details, there was an earlier thread talking on the same question:
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