Hi, these are my very first steps in RNAseq and for the first time in my life I am trying to use a DESeq2 package in R, and I am trying to figure out how can I "sort" my results if I have two tissues (intestine and brain) and for each tissue I have 3 conditions - "control", "black" and "white". Means I have a column "tissue" (for intestine and brain) and I have "state" (for my 3 conditions)
If I understood it well - I have to start from that:
dds <- DESeqDataSetFromMatrix( countData = GeneCounts, colData = colData, design = ~ tissue + state ) dds <- DESeq(dds) res <- results(dds)
That would be the "default" way but when I am trying to do
res1 <- results(dds, contrast=c("tissue","white","control"))
for example for the "white-control" pair I have the following error message:
Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : white and control should be levels of tissue such that tissue_white_vs_brain and tissue_control_vs_brain are contained in 'resultsNames(object)'
Can anyone please explain what that suppose to mean?