False positives due to GC content correction - DESeq2
"Aditi [guest]" <[email protected]>
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
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(): - -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor