Entering edit mode
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
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.
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.
both are yes.
Thank you for your quick reply. Just one more follow-up question - why are the results different?
the values were used in calculation.
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?
p values should be similar, but running score will be different by definition.
Thank you for your answer!