How exactly count numbers are calculated with tximport
Hi all,
I've used tximport for importing the results files of a kallisto alignment like this:
kallisto <- tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreAfterBar = TRUE)
If now I run
kallisto$counts
The resulting matrix is populated with non-integer values. I would've expected raw counts to be integer values. I was wondering how exactly these values are created, but I was not able to find an explanation online. Is it a product of the gene-level summarisation of the transcript-level counts? I'd be really thankful, if someone could explain this to me or point to a resource where it is explained.
Best, Ábris
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jenabris •
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I think your question is explained here, under "Downstream DGE in Bioconductor" section :). So yes, basically decimal numbers are expected since the transcript level information is summarized to the gene-level.
That is why: Raw counts vs expected counts