I've got some microarray datasets which includes Affymetrix probes. I'm using MadGene Tool to map original ids to Uniprot Ids. For most of the Affymetrix probes the tool is not able to identify a correct mapping. I also tried using NetAffx Analysis Center. from the Affymetrix site but I have no results. For some of them the site gives only the go terms associated. Is there a way (a website or a tool) to discover which gene is associated to a particular Affymetrix probe? (I.e AFFX-PheX-5_at or AFFX-BioC-5_at)
Which affymetrix platform specifically are you concerned with? There are many such tools including the two you cite but also Ensembl Biomart, and many others listed here. Likely none of them will successfully map all IDs. Some Affymetrix probe sets just don't map unambiguously to a single gene with our current understanding of the genome. You probably shouldn't use the examples above though since those are control probes (spike-in, house-keeping, off-target-species, etc). Any Affy probe ids starting with AFFX prefix are typically excluded from any analysis and may or may not be included in the various id mapping tools. If you are really interested in the control probes your best bet might be to look up them in the documentation for your specific Affy platform. You might also want to consider using some of the custom CDFs (for example, those created by folks at brainarray) which redefine probe sets for Affy chips using the underlying probe sequences so that you have a new (probably improved) list of probesets which will all map to an actual gene locus unambiguously.
Another approach is to perform your analysis at the probe set level and then when you have identified the most interesting probe sets for you differential expression analysis, classification problem, [use of affy data], then you can spend more effort tracking down what gene, genes or transcripts those probe sets might actually be measuring.