This is a question regarding microarray data pre-processing, which I think is at least partially an issue of terminology.
I recently had a researcher request an analysis involving "normalizing" one sample to another sample, and then the differential expression vs a third sample. This has come up before, when an external collaborator had done something similar with a data set that involved three experimental conditions, to improve sensitivity for a given condition. In that case, they had termed it "delta differential expression". They had used R for their analysis workflow, but I never received the code for that segment.
I believe that this should be theoretically possible in GeneSpring, by performing baseline transformation of arrays for one condition to arrays of another condition, but I am either misinterpreting it or the current version is buggy as it is requiring even samples that have been marked as controls to also have a control set. And that doesn't seem to make any sense.
Perhaps due to the variances in terminology, I haven't been able to find any papers mentioning this, simple as it is. Is there a more common formal name for this? Would it be appropriate to do something as simple as subtracting the mean/median of every probe for the "control" from the probe levels for the other two arrays, and then proceed with the normal DE analysis?