Is it okay to scale the RNA-Seq counts after log-transformation?
Entering edit mode
4.7 years ago

On an RNA-Seq dataset, I want to apply a clustering algorithm which requires zero-mean uni-variance gene expression levels. I am wondering whether it makes sense to use "scale" function in R after taking logarithm of the counts. For microarray data, I was actually using the scale function which (as far as I know) makes sense; but this is the first time I am using RNA-Seq. I heard about "voom" normalization (in "limma" library), but I don't really want to use that since I am not really familiar with the details.

RNA-Seq • 1.0k views

Login before adding your answer.

Traffic: 2179 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6