The usual and fundumental result of the analysis of a microarray data experiment is a list of differentially expressed genes, always according to the statistical design and the biological questions asked. However, what we see most of the times in such a list is a set of differentially expressed probes and not a list of differentially expressed genes (according to official HUGO nomenclature for example). Although this final list contains also gene names next to probes, I have been asked a lot of times to provide a list of genes and discard the probes as they are rather confusing the bench biologists. The latter are asking questions of the type "which probe should I believe" or "why the expression in one probe is so much different from the expression of the other probe corresponding to the same gene"?
The answer is not always easy,
The answer is not always easy,