For proteome differential expression analysis I am using LIMMA. The MassSpec data were quantified by MaxQuant and given to me as a table. For graphical analysis (PCA, clustering) I use VSN (variant stabilising) normalised and batch effective t corrected data.

Now I would like to perform differential expression analysis using LIMMA.

Could you advise me if I should use the original data only or e.g., VSN normalised (BUT NOT BATCH CORRECTED) data as input for limma?

Thank you!