I'm new to BioInformatics and I am working with "benchmark" cancer dataset. I need to retrieve information from GO database, so I'm trying to convert my dataset probe IDs to Uniprot IDs (I'm using MadGene tool). But I have two problems:
1) Some probes are mapped with multiple Uniprot IDs (I.e U70732rna1at -> Q7Z4T9 and P24298). How should I manage this situation? Which Uniprot ID do I have to select for my probe?
2) Sometime different probes are mapped with the same Uniprot IDs? What is the best method to resolve this problem? Should I average the gene expression values of such probes?