Do the count values should be only integer to be able to use DESeq2?
1
0
Entering edit mode
Sep • 0
@06de5a1f
Last seen 8 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 • 1.9k views
ADD COMMENT
0
Entering edit mode
jshouse ▴ 10
@jshouse-10956
Last seen 16 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
1
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?

ADD REPLY
0
Entering edit mode

It is basically NGS. Is it working with DESeq2?

ADD REPLY

Login before adding your answer.

Traffic: 430 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6