HI every one I am new to RNA seq analyisis using R. I Am usig DESeq 2 for my analysis. I have four different Samples with three replicates each and I want to compare all of them with control plk. I tried using contrast but i can only compare two factors using contrast.

condition <- factor(c("bio","bio", "bio","Glu","Glu", "Glu","NO","NO","NO","plk","plk","plk"))

dds <- DESeqDataSetFromMatrix (countData = counts, colData = colData, design = ~condition) res <- results(dds, contrast = c("condition","Glu","bio"))

You can use a numeric contrast, see ?results. You would give numbers to the values in resultsNames(dds). E.g. to compare 1/3 of each you would put 1/3 in the place of the groups you want to average and -1 in the place of the control group, e.g. c(-1,1/3,1/3,1/3).