Do the count values should be only integer to be able to use DESeq2?
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Sepehr • 0
@06de5a1f
Last seen 15 hours ago
Germany

Dear Sir/Madam,

I have a count matrix that values are peptide measurements and they are not integer. I want to ask if we are only able to use DESeq2 if the count matrix is integer and not double?

I got the following error when I am using

dds <- DESeqDataSetFromMatrix(countData = bigdf_t_copy, colData = sample_info, design = ~ Condition)

Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

Thanks a billion for your kind help in advance.

Kind regards,

Sepehr

DESeq2 • 105 views
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jshouse ▴ 10
@jshouse-10956
Last seen 12 days ago
United States

Yes, DESeq2 requires an integer count matrix. For transcriptome counts, rounding to the nearest whole number works. If X is the count matrix; X <- round(X,0).

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Careful. It's not just integers but a type of assay that follows a negative binomial distribution, that is typically digital counts as in RNA-seq or genomic assays such as ATAC-seq. What kind of experiment is this? Something like mass spectrometry?

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It is basically NGS. Is it working with DESeq2?

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