I have a RNA seq dataset with one cell type and 8 different conditions/treatments in triplicates. I would like to compare one of the condition vs the other seven to see expression changes over the different treatments.
I thought I could use the solution offered in this post (https://support.bioconductor.org/p/86347/)
I designed my dds as follows:
ddsAll <- DESeqDataSetFromMatrix( countData = cts, colData = coldata, design = ~ condition )
It works well when I compare treatment 1 vs treatment 2 but when I try to do something like:
res1 <- results (ddsAll, contrast = list ( c("g1"), c('g2','g3','g4','g5','g6','g7')) , listValues=c(1, -1/7))
it gives me this error:
Error in checkContrast(contrast, resNames) : all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'
I tried to see whether someone had similar issues but I could not find anything. Worst case scenario I can do one comparison at a time but it would be great if I could do the analysis to all the samples at once.