[BioC] False positives due to GC content correction - DESeq2

[Aditi [guest]]

Hi Mike,

I have been trying to use DESeq2 for a differential analysis of Chipseq data using 8 T/N pairs. There is a lot of heterogeneity in the samples due to clinical differences ( tumor stage etc), total mapped reads ( some samples are much better than the others), batch effects ( since they were processed at different times and not by the same person). I wanted to correct atleast some of the biases starting with GC content and what I did was to use offsets from EDAseq as an input to DESeq2 and introduced the batch variable in the model.

What I dont understand is that when I corrected for GC bias in the samples, the final results tend to have a lot of false positives. I have attached the dispersion plots for both the runs. I cant seem to figure why


 -- output of sessionInfo(): 

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