How to remove batch effect on DEP protemics package?
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@183232d3
Last seen 3 days ago
Czechia

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..

Proteomics DEP MassSpectrometryData • 66 views
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@2220c3e8
Last seen 9 days ago
Switzerland

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

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