[BioC] Error in summary(hyperGtest)
James W. MacDonald
jmacdon at med.umich.edu
Mon Jul 13 22:57:11 CEST 2009
> p <- new("GOHyperGParams", geneIds=as.numeric(geneIds),
universeGeneIds=as.numeric(GeneIDUniverse), annotation="hgu133plus2.db",
ontology="BP", pvalueCutoff=0.001, conditional=F, testDirection="over")
> hyp <- hyperGTest(p)
> hyp
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: 12592
Annotation package: hgu133plus2
> summary(hyp)
GOBPID Pvalue OddsRatio ExpCount Count Size
1 GO:0009615 6.709096e-13 26.431053 0.60530496 12 103
2 GO:0051707 9.964367e-12 15.220988 1.19297967 14 203
3 GO:0009607 1.123924e-10 11.235085 1.71601017 15 292
4 GO:0051704 3.441994e-08 6.672310 3.01477128 16 513
5 GO:0006955 2.755437e-06 4.963045 3.67296696 15 625
6 GO:0050896 7.513094e-06 3.011330 14.39215375 31 2449
7 GO:0006952 1.018216e-04 4.187715 3.32036213 12 565
8 GO:0019441 1.018268e-04 347.694444 0.01763024 2 3
9 GO:0002376 1.485646e-04 3.433529 5.15978399 15 878
10 GO:0045110 2.028774e-04 173.833333 0.02350699 2 4
11 GO:0006569 3.368410e-04 115.879630 0.02938374 2 5
12 GO:0042436 3.368410e-04 115.879630 0.02938374 2 5
13 GO:0046218 3.368410e-04 115.879630 0.02938374 2 5
14 GO:0060052 3.368410e-04 115.879630 0.02938374 2 5
15 GO:0006334 3.917094e-04 12.948571 0.34672808 4 59
16 GO:0052547 4.451811e-04 12.492231 0.35848158 4 61
17 GO:0044419 5.214595e-04 5.484628 1.41629606 7 241
18 GO:0031497 5.348740e-04 11.864762 0.37611182 4 64
19 GO:0006576 6.367334e-04 11.297052 0.39374206 4 67
20 GO:0034728 6.735437e-04 11.119643 0.39961881 4 68
21 GO:0006568 7.019905e-04 69.516667 0.04113723 2 7
22 GO:0045109 9.324263e-04 57.925926 0.04701398 2 8
Term
1 response to virus
2 response to other organism
3 response to biotic stimulus
4 multi-organism process
5 immune response
6 response to stimulus
7 defense response
8 tryptophan catabolic process to kynurenine
9 immune system process
10 intermediate filament bundle assembly
11 tryptophan catabolic process
12 indole derivative catabolic process
13 indolalkylamine catabolic process
14 neurofilament cytoskeleton organization
15 nucleosome assembly
16 regulation of peptidase activity
17 interspecies interaction between organisms
18 chromatin assembly
19 biogenic amine metabolic process
20 nucleosome organization
21 tryptophan metabolic process
22 intermediate filament organization
> sessionInfo()
R version 2.9.0 (2009-04-17)
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] GO.db_2.2.11 GOstats_2.10.0 graph_1.22.2
[4] Category_2.10.1 hgu133plus2.db_2.2.11 RSQLite_0.7-1
[7] DBI_0.2-4 AnnotationDbi_1.6.1 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.1 RBGL_1.20.0
[5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.5-1
[9] xtable_1.5-5
Have you tried something as simple as restarting R?
Best,
Jim
Fraser Sim wrote:
> 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
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