DE_template_example.Rmd - subset discussion

[lpantano]

DE_template_example.Rmd
• Consider changing template to not subset the data by default:
○ DESeq best practice is to avoid subsetting the data: "Typically, we 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."
○ source: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#if-i-have-multiple-groups-should-i-run-all-together-or-split-into-pairs-of-groups
§ One thing to note however is that apeglm shrinkage is incompatible with contrasts, so depending on the individual study and what comparisons need to be made, shrinkage method may need to be swapped for ashr, which is compatible with contrasts