log2 of normalized counts for further analyzes
1
1
Entering edit mode
Laia ▴ 10
@71ed41e2
Last seen 17 months ago
Spain

Hi

I am running some DESeq2 code and I used the argument "counts(dds, normalized=TRUE)" to obtain the normalized table of counts. I understand that this normalization is taking into account length, RNA composition and deep sequencing.

I don't want to do differential expression. I want to do some regression and elastic net analyses. To do so, I need to work with the normalized counts. However, I don't know if I should apply a log2 to the normalized counts table before working with it, or if I can directly work with this data (if it already has log2, or if I don't need it). I just one to regress the outcome (logistic variable) to a continuous predictor variable (the gene obtained in the normalized counts table).

Do I have to apply log2 to the values of the normalized counts table?

Thanks!

DESeq2 log2 normalized counts • 1.7k views
ADD COMMENT
2
Entering edit mode
@james-w-macdonald-5106
Last seen 23 hours ago
United States

This is covered in the vignette.

ADD COMMENT

Login before adding your answer.

Traffic: 476 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6