[BioC] Proper use of annotation package

[Naxerova, Kamila]

Hi all,

I have a little problem using an annotation package that I know how to work around, but I am wondering how to do it more elegantly and efficiently.

I am analyzing a bunch of Mouse Gene 2.0 ST arrays. I built my own annotation package (with much help from all of you!). I am using Limma and want to look up annotation for diff exp genes provided by topTable(). So it's really a standard situation. On the Bioconductor website, this sequence of commands is suggested (http://www.bioconductor.org/help/workflows/annotation-data/)

tbl <- topTable(efit, coef=2)
ids <- tbl[["ID"]]
entrez <- hgu95av2ENTREZID[ids]

Looks beautiful! But when I try to do the same thing, I get:

tbl<-topTable(fit2all,number=100)
ids <- tbl[["ID"]]
mogene20sttranscriptclusterACCNUM[ids]

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : 
  value for "17549282" not found


This error is evidently generated because some of the ids don't map to any accession numbers. I can work around this by filtering my ids first, but am I doing it wrong? Of course lots of probe ids on the array are not going to map to any accession numbers or symbols or names -- why can't they just come back with NA instead of an error message and abortion of the whole process?

Thanks!
Kamila