Question: deseq2 user defined size factors
0
gravatar for Damian Kao
2.0 years ago by
Damian Kao14k
USA
Damian Kao14k wrote:

Is it possible to skip the estimateSizeFactor step in Deseq2 and define your own size factors? If I just replace the size factor vector with my own values, will the down-stream DE steps use these values? I am pretty new with R so it would be very helpful if I can see some example code on how to do this.

deseq2 • 1.9k views
ADD COMMENTlink modified 2.0 years ago by vchris_ngs4.5k • written 2.0 years ago by Damian Kao14k
2
gravatar for Carlo Yague
2.0 years ago by
Carlo Yague4.1k
Belgium
Carlo Yague4.1k wrote:

Hi,

Short answer : yes and yes !

As for the example code, see my answer here.

or more to the point :

sizeFactors(cds) = c(my_Values)
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Carlo Yague4.1k
2
gravatar for vchris_ngs
2.0 years ago by
vchris_ngs4.5k
Seattle,WA, USA
vchris_ngs4.5k wrote:

Yes you can, that is what I can read from the below link

Take a look here and here

There was a post from where Damian you already replied few years back where I can see Jeremy replied that you can set the size factor manually as well with sizeFactors

dds <- estimatesizefactors(dds)<="" code=""> See DESeq for a description of the use of size factors in the GLM. One should call this function after DESeqDataSet unless size factors are manually specified with sizeFactors. Alternatively, gene-specific normalization factors for each sample can be provided using normalizationFactors which will always preempt sizeFactors in calculations. Internally, the function calls estimateSizeFactorsForMatrix, which provides more details on the calculation.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by vchris_ngs4.5k
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