RPKM to TPM conversion?

Question

[brieannsobieski]

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!

[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

[david.peeney]

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

Answer 1

[Antonio R. Franco]

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

Answer 2

[Kevin Blighe]

Also, Harold Pimmental's blog posting:

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

So, looks like you have it correct.

Kevin