FPKM in DESeq2

rondon

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#1

FPKM in DESeq2

07-08-2015, 09:45 AM

Hi guys, I'm using DESeq2. I'd like to see the FPKM, and It should be easy as
> my_fpkm <- fpkm(dds)
But I need do merge the genes sizes data to dds, and I don't know how to do it. Can anyone help me?
I have a table with genes IDs and genes lengths.

my best regards.

Last edited by rondon; 07-09-2015, 09:13 AM.
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fanli

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#2

07-08-2015, 03:08 PM

Something like this:

Code:

mcols(dds)$basepairs <- gene_sizes[, "length"]

assuming gene_sizes is your table.
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rondon

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#3

07-09-2015, 09:13 AM

That's it! Thank you very much!
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