I have inherited microarray data that was collected from two different cell populations that were analyzed using Rosetta Resolver.

The p value for some of the probes is "zero". I'm trying to understand what that means. What does a "0" p value mean?

There were two biological replicates for each population. The p value for each pairwise comparison (comparing the two populations in each biological sample/replicate) is not zero but then the combined p value shows up as zero. Why is that? I didn't perform these analyses and haven't ever used rosetta resolver. Is there a lower limit cut off for these p values below which the software outputs a "zero".

Thanks. V

Rosetta Resolver isn't a Bioconductor package, so this is not the place for your question. If you want to know something about the inner workings of a commercial software package, shouldn't you be asking the company that produced the product rather than some other unaffiliated group?