Error with DESeq2 about integer number
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AndyQ • 0
@andyq-20909
Last seen 5.7 years ago

Hello everyone I am getting an error from DESeq2 saying that some of my numer ar not integers but I am using counts data directly without any normalization or data transformation so I dont understand why I get this error: These are my data type

>     otu   CTR1    CTR11   CTR12   CTR14   CTR15   CTR16   CTR17   CTR19   CTR2
>     Acidaminococcus   0   0   0   0   0   0   92460950    237775700   75412750
>     Acidiphilium  0   0   0   0   0   0   16651500    0   0
>     Acidovorax    0   0   0   0   0   0   0   0   0
>     Acinetobacter 0   0   0   0   0   0   6489200 0   0

Does anyone can help me understand why I get this error:

> dds<-DESeqDataSetFromMatrix(countData=cts,colData=coldata,design=~condition)
Error in DESeqDataSet(se, design = design, ignoreRank) : 
  some values in assay are not integers

Thanks

deseq2 • 883 views
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@mikelove
Last seen 1 day ago
United States

This test is simply looking to see if there are any values in the matrix that don't give a TRUE for is.integer. So you can investigate your data to see why this may be.

I'm not sure about this data being suitable for DESeq2 just from your example rows. Having a count of 16 million and a count of 0 in the same group would suggest that you have a bimodal distribution, whereas the negative binomial is unimodal.

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