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

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


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.

Golsheed is offline   Reply With Quote
Old 05-11-2015, 11:03 PM   #2
Location: New York

Join Date: Oct 2013
Posts: 20

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.
shunyip is offline   Reply With Quote

express, fpkm, isoform

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