Question

Do the count values should be only integer to be able to use DESeq2?

0

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Sep • 0

@06de5a1f

Last seen 15 months 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 • 2.8k views

ADD COMMENT • link 23 months ago Sep • 0

score 0 · Answer 1 · 2023-01-18

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jshouse ▴ 10

@jshouse-10956

Last seen 23 months 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).

ADD COMMENT • link 23 months ago jshouse ▴ 10

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Entering edit mode

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?