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!