which one should I used to calculate logFC?

pachterlab / sleuth

Differential analysis of RNA-Seq

http://pachterlab.github.io/sleuth

GNU General Public License v3.0

305 stars 95 forks source link

which one should I used to calculate logFC? #222

Open YichaoOU opened 5 years ago

YichaoOU commented 5 years ago

Currently, I'm using transcript_tpm = sleuth_to_matrix(so,"obs_norm","tpm") to get a normalized gene expression matrix and then use log2((transcript_tpm[,"treatment_mean"]+1e-100)/(transcript_tpm[,"control_mean"]+1e-100)) as the logFC.

Is it correct?

Thanks, Yichao