I'm currently analyzing a RNA-Seq data using DESeq2. Looking at the FAQ's in https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, concerning the subset of data, the authors recommend "users to run samples from all groups together, and then use the contrast argument of the results function to extract comparisons of interest after fitting the model using DESeq."
However, they show an example of when to subset: when we have one group that has a within-group variable higher than the remaining groups. Thus, I would like to know if we can use
vegan::betadisper, a function to assess homogeneity of variances within-groups to determine if I should proceed or not with subsetting.
Thanks in advance!