This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RPKM to TPM conversion?

Hi all,

I have read past posts about the equations for these conversions and have come across these:

TPM(i) = ( FPKM(i) / sum ( FPKM  all transcripts ) ) * 10^6
TPM = (((mean transcript length in kilobases) x RPKM) / sum(RPKM all genes)) * 10^6

Can someone point me in a direction that validates these equations? Is there any scholarly articles or data sets with both TPM and RPKM where I can check these equations. I've been checking ncbi geo for a data set with both but can't seem to find one.

Thanks!

rpkm tpm conversion rna rna-seq
• 12,674 views • link
written by brieannsobieski • brieannsobieski

hi! Thank you, I just want to know if there is a way to validate these conversion equations / have other studies used this equation? I have no doubt that its "correct" I just want to ensure its valid before using it in my research

• 1 views • link
written by brieannsobieski • brieannsobieski

hey... did you find any articles citing this equation or the validity of the TPM conversion? I am having the same issue

• 1 views • link
written by david.peeney • david.peeney

2 answers

Give a look to this vídeo that explain the difference between RPKM, FPKM and TPM

• 1 views • link
written by Antonio R. Franco Antonio R. Franco

Also, Harold Pimmental's blog posting:

What the FPKM? A review of RNA-Seq expression units

Screen_Shot_2018_06_21_at_16_27_24

So, looks like you have it correct.

Kevin

• 1 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this