Question: Converting expected counts to TPM values
0
gravatar for bhchiang
15 months ago by
bhchiang0
bhchiang0 wrote:

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

ADD COMMENTlink modified 15 months ago by Kevin Blighe43k • written 15 months ago by bhchiang0
1
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe43k
Republic of Ireland
Kevin Blighe43k wrote:

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

ADD COMMENTlink modified 3 days ago • written 15 months ago by Kevin Blighe43k
1

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.

ADD REPLYlink written 3 days ago by RamRS21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 546 users visited in the last hour