Can anybody tell me if it's legitimate to extract the
Score values from the DiffBind analysis and use them for down-stream analysis? Let's say I want to do GSEA with the H3K4me3 signal in all TSS regions. Could I take the
Score column (which you find directly before the
RPKM column)? Or are those values transformed for a specific method, e.g. edgeR?
For reference, I'm using
DBA_SCORE_TMM_READS_FULL (which I assume is relevant for the calculation of the scores) and
What I can say already is that the outcome is different when using score or RPKM.