Question: Accessing RPM from DESeq2
gravatar for sjj2121
3 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 • 215 views
ADD COMMENTlink modified 3 months ago by ATPoint3.0k • written 3 months ago by sjj21210
gravatar for ATPoint
3 months ago by
ATPoint3.0k 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 3 months ago by ATPoint3.0k
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