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

James W. MacDonald jmacdon at uw.edu
Fri Oct 25 16:16:42 CEST 2013

Hi Sandy,

You cannot do a GO test for unannotated reporters. In other words, if 
you have a probeset that measures some unknown thing, then you cannot 
use that probeset because there won't be any GO terms associated with 

What happens if you do

list1 <- list1[!is.na(list1)]




On Friday, October 25, 2013 8:47:21 AM, Sandy wrote:
> 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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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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