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

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