DESeq2 lfcshrink with one condition vs multiple
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@kirstysawicka-24127
Last seen 4.5 years ago

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?

deseq2 • 571 views
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@mikelove
Last seen 6 hours ago
United States

We don't have a symmetric shrinkage functionality with lfcShrink actually. We found that, from user feedback, the symmetric shrinkage (what we called expanded model matrices in the 2014 paper and software) made for very difficult interpretation of complex designs so we pulled back to only "standard" model matrices and focused on betaPrior=FALSE with lfcShrink. But you can continue to use the old functionality as you have above.

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