Not integers values
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@fsadeghpour1989-20886
Last seen 4.8 years ago

Hello

I am a biologist and beginner in R programming and DEseq but very very interested to learn new stuff. Recently I have received an file.csv (Rna seq reads) from a colleague (Sample names + number of reads for many different genes).

I am trying to follow DEseq tutorial from Input data > Count matrix input: I have been told that the values in the excel files are the read counts corresponding to each gene but there are some decimal values in the file as well.

After dds<- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~condition)

I got this error in R: ![enter image description here][1] Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

I can not use decimals in DEseq? Do I need to do any treatment on the file.csv before importing my data to R, If so could please help me? Thank you very much for your support,

deseq2 • 1.4k views
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@mikelove
Last seen 8 hours ago
United States

You can round the values if these are expected gene counts from eg RSEM or another quantifier. It is important to know exactly how the counts were made, I wouldn’t start to work on a file until someone told me the steps used to produce it.

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