i have an expression dataset(called data.trusted.eset)(affymetrix, hgu133a) which i have preprocessed and filtered and which i used as the input for my limma paired analysis to find DE genes. My basic question is, that i want to use the same expressionSet an an input(exprs(data.trusted.eset)) as a basic argument to a gene network co-regulation analysis,----but instead of probesets as rownames i have to replace them with unique gene symbols. Thus, remove in an appropriate way remove NAs but also duplicates.
affyUniverse <- featureNames(data.trusted.eset)
symbols <- hgu133aSYMBOL[affyUniverse]
symbol.Universe <- unique(as.character(symbols))
My main problem is then how to reduce my expression set with these symbols. Or my approach is totally wrong ?
Any suggestions or ideas would be grateful