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Old 02-01-2017, 09:23 AM   #1
Location: Boston

Join Date: Apr 2009
Posts: 10
Default GAGE update and result analysis

I have recently started to use gage and I am bit confused about the pathway results data.

1) My pathway results after running gage contain 114 pathways (80 of them are NA); however, when I look online at the KEGG website, I find 120 pathways for my organism. Isn't gage able to use the latest version of online data?

2) My greater and less data contains the same list of pathways .. just in inverse order (but completely different p/q values). However, this is a bit confusing: e.g. my differential expressed gene list does not contain any down-regulated genes for one pathway but only contains genes that are up-regulated in the same pathway. Why do these pathways even appear in the less dataset when there is no single gene down-regulated? Since the p/q values are too high, I will discard the pathway anyways - was just wondering why this is listed. And what's the purpose of listing them if all q-values are similar: e.g. 0.9929488953. In this context, what's a general excepted q-value cut-off when it comes to publishing data? Is 0.2 or even 0.5 still accepted?

3) Are pathways with a set.size lower than 10 not considered in the stats?

Any feedback is appreciated! Thanks
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