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Question: ReactomePA gsePathway - a couple of questions regarding the input and output
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gravatar for juls
8 months ago by
juls0
juls0 wrote:

Dear all,

I have a couple of questions regarding the input and output of the gsePathway function: 

1) In the resulting data frame - what is NES, core enrichment and what is the rank?
2) Should I use the fold changes or the log2FC in the gsePathway function?

Thank you very much for your help!

Best,
Julia

ADD COMMENTlink written 8 months ago by juls0
1

for first question, you need to read the GSEA paper http://www.pnas.org/content/102/43/15545.abstract

for the second one, of course you can.

ADD REPLYlink written 8 months ago by Guangchuang Yu800

Thanks for the link. I briefly read the paper related Bioconductor package (http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e) and couldn't find it. 

Relating to the second question: do you mean I can use both? Either FC or log2FC? The results are different. 

 

 

ADD REPLYlink written 8 months ago by juls0

both are yes.
 

ADD REPLYlink written 8 months ago by Guangchuang Yu800

Thank you for your quick reply. Just one more follow-up question - why are the results different?

ADD REPLYlink written 7 months ago by juls0

the values were used in calculation.

ADD REPLYlink written 7 months ago by Guangchuang Yu800

I am sorry - I am not sure I understand correctly. So you are saying I can use both - fold changes as well as log2 fold changes in the gsePathway function - and the results are different due to the way they are used in the calculations? 

 

 

ADD REPLYlink written 7 months ago by juls0

p values should be similar, but running score will be different by definition.

ADD REPLYlink written 7 months ago by Guangchuang Yu800

Thank you for your answer!

ADD REPLYlink written 7 months ago by juls0
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