I spent many hours trying to find this answer, but alas to no avail. I have somalogic proteomics data normalized. I have 2 groups (test and control) I want to find the differential expression between those groups.
Normally for RNAseq I would do something like below.
Can someone show me exactly have to change the code used for RNAseq for proteomics.
Thank you very much in advance!
contr.matrix <- makeContrasts( res = test - control, levels = colnames(design)) contr.matrix vfit <- lmFit(v, design) vfit <- contrasts.fit(vfit, contrasts=contr.matrix) efit <- eBayes(vfit) as.data.frame(topTable(efit,coef = 1,number=Inf))