I have experienced very good results with DESeq2 for my RNASeq analysis. As far as I understand, it is a tool that normalise our data from sequencing to make them comparable.
I have a new project implicating proteins counts.
I have couple of data sets. For each sample we have:
rows with proteins names (instead of genes), with their respective counts.
My goal is again to make a differential expression between treated groups versus controls.
I wonder if I can use DESeq2 to do a differential expression for proteins?
Or if the correcting factor that is used by DESeq2 to correct counts for RNASeq is specific to DNA sequencing and it is not applicable to proteins?
Is there a tool that do the exact same thing as DESeq2 but for proteins?