Hello,

I would like to calculate and extract vst matrix using the following code

dds <- DESeqDataSetFromMatrix(countData=df, 
                                colData=metadata, 
                                design=~group, tidy = TRUE)
matrix=assay(vst(dds, blind=F))

As I am not trying to identify differentially expressed genes between the groups, does it make a difference not to specify any design here (design = ~1) in the final vst matrix?

The function description says that "~ 1 can be used for no design, although users need to remember to switch to another design for differential testing." So I assume it does not significantly impact the vst results without specifying the design?

Thanks in advance!

If you only want the vst then set blind to TRUE so it ignored any design. The ~1 is fine as well.