But mapping and alignment in R? Genome annotation in R? I've worked in 3 institutions with a variety of bioinformaticians and that is something I've never seen. I'd argue that R is an unusual choice for that.
Microarrays yes, but no one (should) really uses those anymore.
Don't get me wrong, I do 50-75% of what I do in R.
Mapping an alignment gets farmed out to C via rsubread, samtools, etc. as far as annotation, anyone who doesn't use GRanges (or vcfanno, bed tools, etc) is insane. (You shouldn't be aligning locally anyways, it's a waste of resources in most cases. The broad migrated their workflow to Google last I heard; we do a lot in BaseSpace.). I actually don't see the point of alignment at all for RNA.
Your data almost certainly has batch effects, you know. At least with arrays the prep was fully standardized. Outside of a few big shops (UBC, the Broad, etc) it's the goddamned Wild West in terms of prep for lots of what we used to do with microarrays, especially RNAseq.
And of course since single cell techniques are newish, nutty ideas like designed experiments are only just beginning to dawn on people. Fisher would be apoplectic.
Microarrays yes, but no one (should) really uses those anymore.
Don't get me wrong, I do 50-75% of what I do in R.