How to make the data compatible for DESeq2?
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20 months ago
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I am trying to do DESeq2 on the dataset GSE202203. I downloaded the data from the server using GSE202203_RawCounts_gene_3207 link. But when I opened the data, it was in fraction number as follows:

dataframe

How do I effectively convert the values compatible for DESeq2 analysis?

Is this way correct? df[,-1] <-round(df[,-1],0)

StringTie counts DESeq2 • 614 views
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You should figure out what values they uploaded. If it's TPM or other normalized values the negative-binomial model DESeq2 assumes about the data won't be true, unfortunately.

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I am using this data from GEO database. The file is given as GSE202203_RawCounts_gene_3207.

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OK, so it's probably estimated gene counts from Salmon. In this case you can use tximport or simply use round as you suggested.

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