[BioC] Error in summary(hyperGtest)

[Fraser Sim]

Here are the geneIds...

> paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "")
[1]
"('5906','3433','51191','91543','6999','3434','8638','10561','3627','10964',
'9636','54809','8339','8344','3437','2537','8346','85441','85236','64108','9
3082','11274','3013','5610','85439','10866','4061','8345','222171','10610','
55008','23586','10417','8343','51251','8519','3017','6890','129607','24138',
'7776','51129','57568','55603','2048','10111','3431','152926','197135','8366
6','51513','4599','54739','167227','10486','8351','116071','54897','1471','7
903','6772','9881','4938','4600','147645','55337','8367','64135','157574','9
1351','4940','219285','87178','57714','6773','3456','4741','94240','55601','
54328','26047','9068','3620','4747','85352','26002','55384','6332','5359','8
5462','4343','84166','54625','8347','23767','3665','27324','8038','4856','57
674','84628','10673','4939')"
>

And this is how I generate my GeneIDUniverse

> GeneIDUniverse = unique(unlist(mget(featureNames(eset),
hgu133plus2ENTREZID )))
> GeneIDUniverse = GeneIDUniverse[!is.na(GeneIDUniverse)]

Thanks,
Fraser

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, July 13, 2009 4:07 PM
To: Fraser Sim
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error in summary(hyperGtest)

Hi Fraser,

Fraser Sim wrote:
> I am using bioconductor to perform a hyperGtest on GO BP annotations. This
> code has worked in the past but I am getting a strange error message from
> the summary method of a hyperGtest-results object.
> 
> Here's the code:
> 
>> params = new("GOHyperGParams",
> +    geneIds = as.numeric(geneIds),
> +    universeGeneIds = as.numeric(GeneIDUniverse), annotation =
> "hgu133plus2",
> +    ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE,
> +    testDirection = "over")
>> x <- hyperGTest(params)
>> x
> Gene to GO BP  test for over-representation 
> 652 GO BP ids tested (22 have p < 0.001)
> Selected gene set size: 74 
>     Gene universe size: 11847 
>     Annotation package: hgu133plus2
>> summary(x)
> Error in if (nrow(df) == 0) { : argument is of length zero

You shouldn't be seeing an error like that; it indicates that you aren't 
getting anything at all returned (if df were a 0-rowed data.frame you 
would just get a warning indicating that fact. The error you see 
indicates that df was NULL).

An example that will replicate this would be nice. You could just give 
the 74 EG IDs you used by

paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "")

And cutting and pasting the output in an email. You could also give the 
code you used to subset your GeneIDUniverse so we can recreate what you 
have done.

Best,

Jim


> 
> Why does summary have this error when it looks like there are 22
categories
> which should be returned?
> 
> Here's my sessionInfo()
> 
> R version 2.9.1 (2009-06-26) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base     
> 
> other attached packages:
>  [1] GOstats_2.10.0        graph_1.22.2          Category_2.10.1      
>  [4] hgu133plus2.db_2.2.11 annaffy_1.16.0        KEGG.db_2.2.11       
>  [7] GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4            
> [10] AnnotationDbi_1.6.1   limma_2.18.2          Biobase_2.4.1        
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.22.0   genefilter_1.24.2 GSEABase_1.6.0    RBGL_1.20.0

> [5] splines_2.9.1     survival_2.35-4   tools_2.9.1       XML_2.3-0

> [9] xtable_1.5-5     
> 
> Thanks,
> Fraser
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826