I'm trying to make a DESeqDataSet for comparing against multiple controls using a design matrix specifying set, group, and batch, where set specifies which set of groups to compare. I want to compare each group vs its control within a set while controlling for batch effects. But sometimes a batch has only one set and other times it has multiple sets.
My design is:
design = ~ Group + Set + Batch
The error I'm getting is:
Error in DESeqDataSet(se, design = design, ignoreRank) : design contains one or more variables with all samples having the same value, remove these variables from the design
Here is a snippet from my design matrix:
I want to compare:
Is it possible to do this?