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?

Thanks

Yes, the MA plot data is the same as reported by dba.report(). The X axis is the "Conc" column, and the Y axis is the "Fold" column. These are all reported in log2 form, so that Fold is simply Conc1-Conc2.

I'm not sure what you mean in the bReduceObject=F line of code?

-Rory

This is an artifact of reporting log values of normalized data. After normalization, some of the values may be less than one and hence will have negative log2 scores. So you are correct that if the normalized read counts for a peak in the replicates of one condition are very small (negative log values), add the counts for the replicates of the other condition are consistently higher, the peak can be identified as being differentially bound (with low FDR).

-Rory