Convert FPKM and RPKM to TPM values

Question

[Sandhiya]

Hi all,

I'm trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning model, but my question is "ALL THESE DATA SHOULD BE IN A COMMON FORMAT "; to do this what's the best solution?

I have two questions:

1) To have a common unit, I should convert these data to tpm ie., fpkm,rpkm to tpm; so that all values are in same format In this case how can I do this conversion?

2) If I decide to use DESeq2 to normalize; then is it right to feed all these different file formats into DESeq2 and uniformly have deseq2 normalized values?

Please help me with this?

Thanks!

Answer 1

[Istvan Albert]

The best way to represent count data should be in the original counts,

All that you have FPKM, RPKM, TPM are transformed measures, that unfortunately, may have lost some information along the way.

Different correction factors may have been applied, thus undoing say a TPM is almost never as easy as reverting the formula.

Is there a way where we can convert TPM to raw read count?

If you do wish to give it a go and revert formulas see the timeless post titled:

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