Can VST be run without runing DESeq or estimateSizeFactors
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A ▴ 40
@a-14337
Last seen 4 days ago
United Kingdom

Hi,

I have generated a DESeq object from matrix as follows:

dds<-DESeqDataSetFromMatrix(countData = counts, colData = sample_data, design = ~ condition)


I also want to use vst counts for downstream analysis - can VST be called without doing anything further to the object generated above? or do i need to run the model by DEseq and/or calling estimateSizeFactors

There are many hundreds of samples and so I would like to access the VST counts without having to run the model.

thank you

DESeq2 • 196 views
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ATpoint ▴ 860
@atpoint-13662
Last seen 7 days ago
Germany

Just run it, the necessary steps are taken care of internally. You do not have to do anything other than vst().

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Right, you can just call vst and it will call estimateSizeFactors within the function. Or if you've already estimated or supplied size factors, these will be used.

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thank you all