Hi, I have a doubt regarding contrasts. In my case, i understood,the 1st coefficient is comparison of MHO with MHNW, 2nd coefficient is comparison of MAO with MHNW and 3rd coefficient is comparison of MAO with MHW . Please let me know, if I understood wrong. Please find my code below.
design.adipose = model.matrix(~0+AdiposeCPMCountGT1_min20percentsamples$samples$group.1+AdiposeCPMCountGT1_min20percentsamples$samples$Gender) # To rename column names colnames(design.adipose) = "MAO" colnames(design.adipose) = "MHNW" colnames(design.adipose) = "MHO" colnames(design.adipose) = "Gender" # To do comparisons between groups contr.matrix.Adipose = makeContrasts(MHOvsMHNW = MHO-MHNW,MAOvsMHNW = MAO-MHNW,MAOvsMHO = MAO-MHO,levels = colnames(design.adipose)[1:4]) # Voom function v = voom(AdiposeDGE,design.adipose,lib.size = colSums(AdiposeDGE$counts)*AdiposeDGE$samples$norm.factors,normalize.method="quantile",plot = TRUE)