Hello.

I'm doing some microarray analysis, and I figured out that some probe ids have not any GENE SYMBOL. Am I suppose to delete those probes or let them exist ?

The way I apply annotation info for an Affymetrix HGU133plus2 array after RMA application, is the following:

    probes=row.names(expressions)
    Symbols = unlist(mget(probes, hgu133plus2SYMBOL, ifnotfound=NA))
    Entrez_IDs = unlist(mget(probes, hgu133plus2ENTREZID, ifnotfound=NA))
    expressions=cbind(probes,Symbols,Entrez_IDs,expressions)

Is something wrong with my code or such behavior is expected ? What do you guys do with these NA genes ?


 

It’s not unusual in older array. Due to changes in gene annotation and reference sequence, some probe set may be outdated (probes not mapping to any gene in the new build). To find a gene for your probe set, you need to blat all the probes of the probe set and look where they are mapping. ​