I am using DESeq2 to analyse a dataset with 22 different cell types and I want to compare each cell type with all others. I have been using the following script:
dds <- DESeqDataSetFromMatrix(counts.filtered, colData = colData, design = ~ CellType) dds <- DESeq(dds, betaPrior=TRUE) DGE <- results(dds, contrast=list(CellTypeA, other.CellTypes), listValues = c(1, -1/21))
where other.CellTypes is a vector with the names of all the other 21 cell types.
This works fine. My question is how to set up with same comparison without betaPrior=TRUE so that I can use lfcshrink and the newer shrinkage estimator functions?