I want to clarify what is going on under the hood when a user runs
DESeq2::estimateSizeFactors() with the
controlGenes argument. So, if my understanding is correct, all the steps of size-factor estimation take place, except they are applied only to the genes assigned to
controlGenes (except for the final step, which is to apply the calculated size factor to all sample-wise genes) rather than the default of all genes supplied to
DESeq2::estimateSizeFactors()—is that right?
A related follow up question: Are there any circumstances in which a user that has spike-in
controlGenes for their samples would not want to use them?