I use deseq2 to compare the transcriptomic signatures of 3 cell types composing the same tissue (A, B, C). The object "res" returns only the comparaison between two cell types?

How to obtain other comparisons and in particular the multiple comparison A type vs B type vs C type?

dds <- DESeqDataSetFromMatrix(countData = cts,colData = coldata, design = ~ type) dds colData(dds) dds <- DESeq(dds) res <- results(dds)

res log2 fold change (MLE): type A vs B Wald test p-value: type A vs B DataFrame with 22915 rows and 6 columns baseMean log2FoldChange lfcSE stat pvaluep padj <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> ENSBTAT00000000005.5 136.38480133345 -0.91243490364398 0.404577528126755 -2.25527825993863 0.0241158683357636 0.0519280166333744

If you have questions about how a particular function works in R, the best way to go is look up the help page for that function:

?results

And see the contrast argument in particular. Also this is discussed in the vignette.