Question: DESeq and checkFullRank(modelMatrix)
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6 months ago by
Merlin 10
Vancouver
Merlin 10 wrote:

Hello guys,

I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line.

dds = DESeqDataSetFromMatrix(countData = countMatrix, colData = coldata, design = ~ group + treatment +group:treatment)


although I found online many others people solved the same problem, I couldn't solve by myself. The error that I get is this

Error in checkFullRank(modelMatrix) :
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.


Do you have suggestions on how to solve this?

Thank you

deseq2 rna • 189 views
modified 6 months ago by Michael Love25k • written 6 months ago by Merlin 10
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6 months ago by
Michael Love25k
United States
Michael Love25k wrote:

The vignette has suggestions on this. There’s a section devoted to this design error.