Question: RPKM to TPM conversion?
0
gravatar for brieannsobieski
4 months ago by
brieannsobieski0 wrote:

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!

rna rna-seq conversion tpm rpkm • 439 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by brieannsobieski0

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

ADD REPLYlink written 4 months ago by brieannsobieski0
0
gravatar for Antonio R. Franco
4 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.9k wrote:

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

ADD COMMENTlink written 4 months ago by Antonio R. Franco3.9k
0
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe32k
Republic of Ireland
Kevin Blighe32k wrote:

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

ADD COMMENTlink written 4 months ago by Kevin Blighe32k

An update (6th October 2018):

You should abandon RPKM / FPKM. They are not ideal where cross-sample differential expression analysis is your aim; indeed, they render samples incomparable via differential expression analysis:

Please read this: A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

The Total Count and RPKM [FPKM] normalization methods, both of which are still widely in use, are ineffective and should be definitively abandoned in the context of differential analysis.

Also, by Harold Pimental: What the FPKM? A review of RNA-Seq expression units

The first thing one should remember is that without between sample normalization (a topic for a later post), NONE of these units are comparable across experiments. This is a result of RNA-Seq being a relative measurement, not an absolute one.

ADD REPLYlink written 5 weeks ago by Kevin Blighe32k
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