Hello,

I would like to clarify what are the units of the "Conc" columns and also the read counts column if we set bCounts=T.

For my analysis, I performed dba.count() with score=DBA_SCORE_RPKM and dba.analyze() with method=DBA_DESEQ2.

When I call dba.report(DBA, contrast = 1, th=0.05, fold = 1.5, bCalled = T, bCalledDetail =  T, bCounts = T)

1. Are the concentrations and read count columns reported in log RPKM, or, log raw read counts normalized by sample with smallest library size?
2. Are the concentrations and read counts reported subtracted by the corresponding input sample? 

Thanks for your time and clarification! Appreciate it

Cheers,

Shamaine 

If you called dba.analyze() with defaults (method=DBA_DESEQ2, bFullLibrarySize=TRUE, bSubControl=TRUE), then the read counts have the control reads subtracted, are set to a minimum value of 1, and then normalized to the smallest library size. They are not reported as logs nor as RPKM values.

The concentration values are calculated by taking the mean normalized read count over either all the samples or the samples in a group, and reported as log2() values.