[BioC] Error in extracting genes from Goterms using GOStats package

Sandy deschisandy at gmail.com
Fri Oct 25 14:47:21 CEST 2013

Hi James, 

probeSetSummary2(hgOver) works well as long as there are no NA's in this 
particuar step:

list1<- (unlist(mget(selectedgenes,ath1121501ACCNUM,)))

In the presence of NA's, then probeSetSummary2(hgOver) gives me this warning

Warning message:
The vector of geneIds used to create the GOHyperGParamsobject was not a 
named vector.
If you want to know the probesets that contributed to this result
either use a named vector for gene Ids, or pass a vector of probeset IDs
via sigProbesets.

And then most GO terms go missing in the result.

What do I do in such a case?

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