Hi,

How could we test for linear combinations between variables added to the model before running "DESeq()"?

It would be nice if we could detect vars with lin. comb. and remove them beforehand.

We basically would like to protect against this error before calling "DESeq()":

"Error in DESeqDataSet(se, design = design, ignoreRank) :
  the model matrix is not full rank, so the model cannot be fit as specified.
  one or more variables or interaction terms in the design formula
  are linear combinations of the others and must be removed
Calls: DESeqDataSetFromMatrix -> DESeqDataSet"
Execution halted

Many thanks

You can look at the rank of the design matrix using model.matrix(design(dds), colData(dds)) and qr(x)$rank.