Hi again, sorry lots of questions at the moment,
I would like to replicate the following function from diffBind
> dba.plotMA(tamoxifen, bXY=TRUE)
However I don't know how to retrieve this data, in Deseq2 I believe it would be the baseMean column. Or is the "Conc" column output by "dab.report" the values used for the plot ma?
I know one option would be:
> DBA$contrasts[[n]]$DESeq2$DEdata, bReduceObjects=F
Where I assume DBA is the DBA object, but what is "n"??
Also, on a separate note, is the "Fold" column output by "dba.report" as default the log2 fold values?