How to import a csv file as DESeq2 object which contains non-integers value?
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5 weeks ago
arriyaz.nstu ▴ 30

I have a data set in CSV format which contains non-integer values as shown in the following figure:

enter image description here

I guess this is a normalized version of the original read count table. So, when I tried to import this dataset as DESeq2 object I got the following error:

enter image description here

As I can understand, this error is trying to tell me to insert the original read count. But I don't have the original read count table.

Would you please suggest me, how I can import this CSV file as a DESeq2 object?

Thanks in advance.

DESeq2 RNA-seq • 180 views
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This has been asked so many times before. DESeq2 takes raw counts and if you don't have them don't use DESeq2. If you only have normalized counts from RNA-seq then log2-transform them and use limma-trend, see limma manual for that. By the way, and I can only speak for myself, but I would never do an analysis based on guesses. Either get the fastq files or at least the raw count table (including code how it was created) or reject the analysis.

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What is your purpose ? If you want to perform differential analysis, without raw counts you won't be able to use DESeq() : https://support.bioconductor.org/p/83769/

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