I have a differential gene expression experiment, and get out microarray probe IDs with p-values and fold changes.
I can map them to the Entrez Gene IDs using the standard annotation platforms or the Ensembl ID mapper. However, consider the following situation:
- gene gA has got associated probes pA and pB
- gene gB has got associated probes pB and pC
- probes pA and pB show significant upregulation, pC no change
In this case, it is likely that gA is upregulated and gB is not. But if I, like is often the case, take the smallest p-value, I would assume that both gA and gB are upregulated.
So, my questions are:
- how likely is it that such a situation occurs in a given DE experiment (vs., e.g. splice variants)?
- are there tools that address this?