How can I convert the GSE121 that have multiple platform GPL80, GPL98, GPL99, GPL100, GPL101 into expression with the feature names are annotated to ENTREZ id instead of the original probe id? can someone help me with that...and I wanna do it in R/bioconductor. I've tried using GEOquery but I couldnt get it..not sure whether my method is wrong..plz help..
You might be interested in this recent paper. Not a BioC solution, but seemingly aimed at what you want to do:
"MADGene is a software environment comprising a web-based database and a java application. This platform aims at unifying gene identifiers (ids) and performing gene set analysis. MADGene allows the user to perform inter-conversion of clone and gene ids over a large range of nomenclatures relative to 17 species. We propose a set of 23 functions to facilitate the analysis of gene sets and we give two microarray applications to show how MADGene can be used to conduct meta-analyses."