Question

GAGE function and the same.dir option

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Aurora ▴ 20

@aurora-15104

Last seen 5.5 years ago

Good morning,

I am trying to find perturbed pathway from expression date using a kegg gene set.

In the GAGE paper (Luo et al., 2009), iit is recommanded to use the option same.dir=F on KEGG pathwayt is worthy to run gage with to capture pathways perturbed towards both directions simultaneously.

With the option same.dir=F, I only get in the results the part "greater", but when I use same.dir =F, I have completely different pathways and i have a part "greater" and a part "less".

I don't know how to interpret these results.

Using same.dir=F, how can i know if the pathway is upregulated or downregulated ? why do I get different results changing this option?

Thank you for your response

gage gene set testing • 1.3k views

ADD COMMENT • link updated 5.9 years ago by Luo Weijun ★ 1.6k • written 5.9 years ago by Aurora ▴ 20

score 0 · Answer 1 · 2018-05-28

same.dir=T tests for pathways with genes changing towards one direction. Greater and less components in the results correspond to tests for up and down regulated pathways respectively. same.dir=F tests for pathways where genes change towards both directions at the same time. There is only greater but no less component in the results, i.e. pathways that are more perturbed (than expected) in the tests. All of these are described in the package documentation and vignette.