Hi,

I'm doing the analysis of "mass spectrometry" data (Max-quant- Intensity values) by using DEP package. I have a batch effect on my data. Is there any way to take care of the batch effect in DEP package (https://www.bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html). I know there is a batch server that takes care of such a problem but i'm looking for something within the package. Can you please suggest something..

Within the DEP package, I don't know. I guess read the vignette. In transcriptomics ComBat or removeBatchEffect (Limma package) is widely used.