Question: Error when creating a DESeqDataSet object
0
gravatar for colaneri
6 weeks ago by
colaneri30
United States
colaneri30 wrote:

Hi I have a RNAseq experiment with 2 genotypes (Wt vs Mut) and 2 conditions (treat untreat)

I like to run a interaction test and I created the dds object with the below command:

dds <- DESeqDataSet(se, design= ~genotype + genotype:treatment)

However I got the below error, which I was trying to track in the web but I found nothing.

Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class "CompressedGRangesList" is not valid for slot 'rowRanges' in an object of class "DESeqDataSet"; is(value, "GenomicRanges_OR_GRangesList") is not TRUE

I can not figure out what is going on. I updated all packages but the error still there. I downloaded the airway data and everything since to work ok with that data

deseq2 deseqdataset • 54 views
ADD COMMENTlink modified 6 weeks ago by Michael Love23k • written 6 weeks ago by colaneri30
Answer: Error when creating a DESeqDataSet object
0
gravatar for Michael Love
6 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

Check BiocManager::valid() and if there are errors follow the suggestions.

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Michael Love23k

Thank you Michael Problem solved!

ADD REPLYlink written 6 weeks ago by colaneri30
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