DESeq2 estimateSizeFactors with control genes
2
0
Entering edit mode
cris.kgs • 0
@criskgs-18612
Last seen 5.9 years ago

I am using DESeq2 for a while now, but I never see people talking about the use of the function "estimateSizeFactors" with the option  "controlGenes".

For what I understand, it is supposed to be used with spike-ins, in which case DESeq2 will estimate the size factors only with the spike-ins and use it to normalize the counts of the other genes. 

In my case, I am suspecting a global shift in gene expression, so is it correct to use internal controls (instead of spike-ins) in the option "controlGenes"? Or would you say that a global shift negates the premise of the algorithm?

deseq2 differential gene expression controls references • 5.0k views
ADD COMMENT
1
Entering edit mode
mahesh ▴ 10
@mahesh-18622
Last seen 5.9 years ago
New York, USA

Usage: 

Example Code Looks Like:

This would be the Helpful link for you. 

Check this out: https://rdrr.io/bioc/DESeq2/man/estimateSizeFactors.html

Regards;

Visit for Dog Sneezing Issues.

ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 hour ago
United States

 I know lots of groups that use this argument with endogenous features for example housekeeping promoters or genes.  This is part of its intended usage 

ADD COMMENT

Login before adding your answer.

Traffic: 939 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