Question: Accessing RPM from DESeq2
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gravatar for sjj2121
14 days ago by
sjj21210
sjj21210 wrote:

Hi,

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 • 131 views
ADD COMMENTlink modified 14 days ago by ATPoint2.5k • written 14 days ago by sjj21210
0
gravatar for ATPoint
14 days ago by
ATPoint2.5k
Germany
ATPoint2.5k 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 14 days ago by ATPoint2.5k
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