Question: Accessing RPM from DESeq2
gravatar for sjj2121
10 months ago by
sjj21210 wrote:


This may be a simple question but I've been stumped trying to find the right set of commands to do this, but is there a way to extract a RPM matrix from a dds object in DESeq2? I was able to make the dds object and did some preliminary PCA plotting of based on the rlog transform of the genes, but now I want to use the RPM to do some analysis of my samples that isn't strictly differential expression. Is there a command to do this or should I just take my original counts matrix and do the calculation myself? (Pretty new to R and this kind of analysis so any help is appreciated!)

rna-seq deseq • 493 views
ADD COMMENTlink modified 10 months ago by ATpoint7.5k • written 10 months ago by sjj21210
gravatar for ATpoint
10 months ago by
ATpoint7.5k wrote:
counts(dds, normalized=TRUE)

Double check here. Note that this is not RPM but the result of the DESeq2 geometric mean normalization.

ADD COMMENTlink written 10 months ago by ATpoint7.5k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 583 users visited in the last hour