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Cufffdiff returns 0 conf_low fpkm and high conf_hi fpkm for EVERY gene fattest0828 Bioinformatics 0 02-03-2015 03:31 AM
the gene fpkm and isoform fpkm are zero with Cufflink ??? fulxie RNA Sequencing 5 05-10-2012 12:41 AM

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Old 05-11-2015, 03:22 PM   #1
Golsheed
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Location: Montreal

Join Date: Oct 2014
Posts: 49
Default gene FPKM from eXpress

Hello,

I want to calculate gene-level FPKM values from eXpress data. From eXpress output, I have FPKM values for each isoform of a gene.

(1) Can I just sum the FPKM values for all isoforms of a given gene to get that gene's FPKM value? If not, what's the correct way to do that?

(2) If the above-mentioned method is correct, can someone please briefly
explain why it works?

Any help is much appreciated.

Thanks,
Golsheed
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Old 05-11-2015, 11:03 PM   #2
shunyip
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Default

No, it doesn't work. Please look at FPKM's formula.

Instead, you should sum up the raw counts of your gene and then use it to calculate its FPKM.
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