How to prepare GSEA Pre-Ranked input file
Dear Biostars, I have a file representing correlation values of certain genes (row) and transcription factors binding sites (colums). I would like to convert this file as a Pre-ranked file and submit to GSEA. Any suggestions would be appreciated.
ex:
name tf1 tf2 tf3
gene1 0.8 0.4 0.2
gene2 -0.2 -0.6 -0.7
gene3 0.1 0.6 0.8
gene4 0.1 0 0
gene5 -0.2 -0.2 -0.2
gene6 -0.1 -0.9 -0.9
gene7 0 0 0.2
1 answer
Well you will need to apply a statistic, say a t-test to come up with a p-value for each row.
See this post as well: Gsea Pre-Ranked File Format
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Istvan Albert
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