How to obtain FDR across all regions investigated in DiffBind
I'm interested to make a Volcano plot and using different color i want to show which genes are UP and which are DOWN.
To do this I need to use the logFc and FDR relative to ALL investigated regions and not just of DEGs.
While logFC was found in in this way:
dbObj_region <- dba.analyze(dbObj_region, method=DBA_EDGER) b <- dbObj_region$contrasts all_site <- as.data.frame(b[]$edgeR$LRT$table)
I can't find FDR value of all sites.
Can you help me??
Thanks a lot
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Could it be as simple as:
? Your code isn't quite clear (to me), but if edgeR is used in the process, and I'm guessing that last line returns a typical edgeR table containing all the things investigated, then a typical way to adjust p-values (i.e. examine FDR) is to use the p.adjust function).