I have a question about the dba.report() output when setting  bCounts=TRUE. What are the values blow each samples mean?

In the default case, where bNormalised=TRUE, the values are the normalised read counts that are used by the analysis package. If, in the call to dba.analyze(), bSubControl=TRUE (default), the number of reads in the control are subtracted first, with a minimum read count of 1 before normalisation.

If you set bSubControl=FALSE when calling dba.analyze(),it will use the actual read counts (minimum 1), and if you set bNormalised=FALSE, it will report the actual number of reads for the sample for the peak interval represented by the row.

Cheers-

Rory