Question: DESeq and checkFullRank(modelMatrix)
0
gravatar for Merlin
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
ADD COMMENTlink modified 6 months ago by Michael Love25k • written 6 months ago by Merlin 10
Answer: DESeq and checkFullRank(modelMatrix)
0
gravatar for Michael Love
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.

ADD COMMENTlink written 6 months ago by Michael Love25k

Also I notice that many of our past interactions involve me suggesting you to read certain parts of the vignette. At this point I think it would be reasonable for you to first check the entire vignette and the function help pages before posting a support site question.

ADD REPLYlink written 6 months ago by Michael Love25k
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