I used to first normalize Affymetrix microarray data with RMA by 'probeset':
oligo::rma(rawData, background=TRUE, normalize=TRUE, target="probeset")
and then convert probe ids to gene ids with:
select(microarrayPackage, keys = as.character(ids), column = c('PROBEID','ENSEMBL'), keytype='PROBEID')
But now some annotations that used to be '.db' were replaced by 'transcriptcluster.db' and 'probeset.db'. Can I run exactly same code using the 'probeset.db' ? or should I use 'transcriptcluster'?
I know there is a post on this, but still I can't understand if when running code above I should use one or the other.