Hello,

I have never used PathFindR, but from looking at the tutorial here: Enrichment Analysis, Clustering and Scoring with pathfindR

It looks like you need to provide the output of an RNA-seq comparison generated from DESeq2 or other DGE analysis package (EdgeR?). Check out the tutorial I linked above...

If you can see... the input for PathFindR looks something like this:

head(RA_input)

  Gene.symbol    logFC  adj.P.Val
1     FAM110A -0.69394 3.4087e-06
2      RNASE2  1.35350 1.0085e-05
3      S100A8  1.54483 3.4664e-05
4      S100A9  1.02809 2.2626e-04
5      TEX261 -0.32360 2.2626e-04
6    ARHGAP17 -0.69193 2.7081e-04

This would be the standard output of DESeq2 (except that logFC would be log2FC). Maybe someone else could chime in here as well, with regard to using LogFC or Log2FC?