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2 hours ago by

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.



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