I have a list of differentially expressed probesets on one microarray platform. Many of these probesets map to more than one transcript, and there are some transcripts measured by more than one probeset on the platform (many to many mapping).
I have performed differential expression analysis at the probeset level on another platform, with all probesets only mapping to one transcript, but some transcripts measured by multiple probesets (many probes to one transcript). These 2 platforms do not measure the same population of transcripts but have some overlap.
I am interested to see if the lists of differentially expressed transcripts (with concordant direction), as determined by mapping from differentially expressed probesets on each platform, significantly overlap between the two platforms. Is there any way to do this with the current experiment design (without a 1 to 1 mapping)?