I would like to look at the differential expression of three groups- all with the same condition. Most resources I found focus on two-group comparison or two condition and two group comparison. I have not found anything for one condition and three group comparisons.
For example, I want to know what genes differ among three types of cells- type A, type B, and type C. I found suggestions to set up three separate pairwise comparisons (A/B, A/C, B/C), but would like to set up one three-group comparison (A/B/C) to determine which genes are unique to each cell type.
I have looked into using the contrast argument of the results function to extract comparisons, but get the error “(Type A) should be the name of a factor in the colData of the DESeqDataSet.”
dds <- DESeqDataSetFromMatrix(counts, DataFrame(groups), ~groups) dds <- DESeq(dds) res <- results(dds, contrast = c("Type A", "Type B", "Type C"))
Any advice is appreciated!