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
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
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
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
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.