Question: duplicate genes in Affy arrays
14.4 years ago by
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Is there any general procedure for handling duplicate genes in Affy arrays? For example, for the hu6800 array which has 7129 probe sets, there are 869 genes that are represented by more than one probe set, with one gene (ACTB) being represented by 9 probe sets. g.symbols=aafSymbol(X.gnames,"hu6800") ug.symbols <- unlist(g.symbols) length(ug.symbols) #6980 (7129-6980 = 149 with no symbols) symbol.usage <- table(ug.symbols) sum(symbol.usage>1) # 869 max(symbol.usage) #9 Ignoring this would seem to invalidate a number of multiple comparison procedures. Is it reasonable to average probe set expression levels for the same gene? Are there any "pre-processing" routines that address this issue? The flip side of this question is "Do probe sets with the same gene symbol really specify the same gene? Does it matter which annotational method is used to name genes?"
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