Dear all,

I am working with a DESEQ2 object and when I run dds0 <- DESeq(dds0) it works fine for the type "arm" as specified here:

dds0_sub <- dds0[,dds0$Sample.Site == "arm"]

But if I do the same with "leg"

dds0_sub <- dds0[,dds0$Sample.Site == "leg"] and dds0 <- DESeq(dds0) I get the following error:

Error in designAndArgChecker(object, betaPrior) : 
  full model matrix is less than full rank

Has anyone an idea what it could be?

Thank you, Bine

DESeq2 relies on model.matrix from base R, which doesn't want factors to have levels with no samples:

table(dds$variable)

You can resolve this by running droplevels on the column and re-saving it to the colData of dds with the paradigm dds$variable <- ....