Converting expected counts to TPM values

Question

[bhchiang]

I want to obtain TPM values for MCF-10A RNA-seq. Does anybody know to convert expected counts values to TPM values? Thanks so much!

Link to expected counts: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71862

Answer 1

[Kevin Blighe]

Edited June 12, 2019

The 'expected counts' to which you refer are derived via the RSEM algorithm, which should also produce TPM counts. However, the dataset to which you have linked appears to only provide expected counts - you can use these as input to, e.g., DESeq2, for the purposes of normalisation (you will have to round them to integers, first).

Further reading: https://biowize.wordpress.com/2014/03/04/understanding-rsem-raw-read-counts-vs-expected-counts/

Kevin

[Ram]

I think one would need the transcripts' effective length calculated by RSEM to have any hope of calculating the FPKM/TPM values from the expected counts.