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Old 04-18-2019, 05:22 AM   #1
Location: Italy

Join Date: Jul 2017
Posts: 34
Default DESeq and checkFullRank(modelMatrix)

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
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