How to import a csv file as DESeq2 object which contains non-integers value?

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2.4 years ago

Anisur Rahman ▴ 80

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 • 1.4k views

ADD COMMENT • link updated 2.4 years ago by lieven.sterck 15k • written 2.4 years ago by Anisur Rahman ▴ 80

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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.

ADD REPLY • link 2.4 years ago by ATpoint 85k

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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/

ADD REPLY • link 2.4 years ago by Basti ★ 2.0k

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