How to make the data compatible for DESeq2?
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:
How do I effectively convert the values compatible for DESeq2 analysis?
Is this way correct?
df[,-1] <-round(df[,-1],0)
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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.
I am using this data from GEO database. The file is given as
GSE202203_RawCounts_gene_3207.OK, so it's probably estimated gene counts from Salmon. In this case you can use tximport or simply use
roundas you suggested.