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Question: DESeq2 estimateSizeFactors with control genes
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12 days 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?

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modified 11 days ago by mahesh0 • written 12 days ago by cris.kgs0
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12 days ago by
Michael Love20k
United States
Michael Love20k 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 12 days ago by Michael Love20k
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11 days ago by
mahesh0
New York, USA
mahesh0 wrote:

Usage:

• ## S4 method for signature 'DESeqDataSet'
estimateSizeFactors(object, type = c("ratio",
"poscounts", "iterate"), locfunc = stats::median, geoMeans,
controlGenes, normMatrix, quiet = FALSE)

Example Code Looks Like:

• dds <- makeExampleDESeqDataSet(n=1000, m=4)
dds <- estimateSizeFactors(dds)
sizeFactors(dds)

dds <- estimateSizeFactors(dds, controlGenes=1:200)

m <- matrix(runif(1000 * 4, .5, 1.5), ncol=4)
dds <- estimateSizeFactors(dds, normMatrix=m)
normalizationFactors(dds)[1:3,]

geoMeans <- exp(rowMeans(log(counts(dds))))
dds <- estimateSizeFactors(dds,geoMeans=geoMeans)
sizeFactors(dds)

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 COMMENTlink written 11 days ago by mahesh0
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