Question: Is it possible to get the results after TMM normalization in edgeR?
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gravatar for statmushroom
3 days ago by
statmushroom0 wrote:

I only get the normal factor with dge$samples; how can i get the exact values after the TMM normalization?

rna-seq R • 75 views
ADD COMMENTlink modified 3 days ago by Kevin Blighe59k • written 3 days ago by statmushroom0
3
gravatar for Kevin Blighe
3 days ago by
Kevin Blighe59k
Kevin Blighe59k wrote:

You may want to search around Biostars and Bioconductor for how to do this and what it means. For a 'philosophical' initial discussion, please read the answers by James and Gordon: Method to get normalized counts in edgeR without cpm.

Lately, as I have been answering many questions on RNA-seq analyses, and in knowing the vagueness of the meaning of the words, I have also somewhat shuddered inside when writing out the words 'normalised count' (or with a 'z', if you're American / Canadian).

Eventually, after searching, you may stumble upon this answer, which should allow you to get what you want: edgeR TMM values.

Kevin

ADD COMMENTlink modified 3 days ago • written 3 days ago by Kevin Blighe59k
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