I'm dealing with Illumina HT12 v4 BeadChip data, I understand that there are replicate probes on the arrays, but these replicate probes have a different nuID and hence a different probe sequence attached to the bead. Has anyone seen any literature or knows off the top of their head, if these replicate probes have different sequences for different transcript variants or just a different binding site of the parent transcript?
Ultimately I'm trying to gauge what the effect is if a given gene X has one probe that's differentially expressed and has 2 others that are not differentially expressed. Biologically and statistically.
Any input is appreciated!