Taking scores from DiffBind for other analysis?

Question

[Roman Hillje]

Hi guys,

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 DBA_EDGER.

What I can say already is that the outcome is different when using score or RPKM.

Thanks!