Question: DESeq2 estimateSizeFactors with control genes
0
gravatar for cris.kgs
7 months ago by
cris.kgs0
cris.kgs0 wrote:

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?

ADD COMMENTlink modified 7 months ago by mahesh0 • written 7 months ago by cris.kgs0
Answer: DESeq2 estimateSizeFactors with control genes
0
gravatar for Michael Love
7 months ago by
Michael Love24k
United States
Michael Love24k wrote:

 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 COMMENTlink written 7 months ago by Michael Love24k
Answer: DESeq2 estimateSizeFactors with control genes
0
gravatar for mahesh
7 months ago by
mahesh0
New York, USA
mahesh0 wrote:

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;

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ADD COMMENTlink written 7 months ago by mahesh0
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