Question: Converting expected counts to TPM values
0
gravatar for bhchiang
2.8 years 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 2.7 years ago by Kevin Blighe67k • written 2.8 years ago by bhchiang0
1
gravatar for Kevin Blighe
2.7 years ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k 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 17 months ago • written 2.7 years ago by Kevin Blighe67k
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 17 months ago by RamRS30k
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