Entering edit mode
Hi all,
I recently updated to R 2.8. I have a list of significant genes and
want to do hypergeometric test to check for over-representing
pathways and ontologies.
For KEGG it works fine but for GO I got the following error:
any help will be appreciated!!!
>params <- new("KEGGHyperGParams", geneIds = eids, universeGeneIds =
universe, annotation = lib, pvalueCutoff=1)
> params2 <- new("GOHyperGParams", geneIds = eids, universeGeneIds =
universe,
+ annotation = lib, ontology = ontology, conditional=cond,
pvalueCutoff=1)
> hyperGTest(params)
Gene to KEGG test for over-representation
116 KEGG ids tested (116 have p < 1)
Selected gene set size: 139
Gene universe size: 3166
Annotation package: hgu133a2
> hyperGTest(params2)
Error in initialize(value, ...) :
invalid names for slots of class "GOHyperGResult": pvalues,
oddsRatios, expectedCounts, catToGeneId
> str(params)
Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots
..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ...
..@ universeGeneIds : chr(0)
..@ annotation : chr "hgu133a2"
..@ datPkg :Formal class 'AffyDatPkg' [package
"Category"] with 1 slots
.. .. ..@ name: chr "hgu133a2"
..@ cateogrySubsetIds: NULL
..@ categoryName : chr "KEGG"
..@ pvalueCutoff : num 1
..@ testDirection : chr "over"
> str(params2)
Formal class 'GOHyperGParams' [package "Category"] with 10 slots
..@ ontology : chr "BP"
..@ conditional : logi TRUE
..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ...
..@ universeGeneIds : chr(0)
..@ annotation : chr "hgu133a2"
..@ datPkg :Formal class 'AffyDatPkg' [package
"Category"] with 1 slots
.. .. ..@ name: chr "hgu133a2"
..@ cateogrySubsetIds: NULL
..@ categoryName : chr "GO"
..@ pvalueCutoff : num 1
..@ testDirection : chr "over"
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets methods base
other attached packages:
[1] statmod_1.3.8 GOstats_2.8.0
RBGL_1.18.0 Category_2.8.4 annaffy_1.14.0
[6] KEGG.db_2.2.5 GO.db_2.2.5
hgu133a2probe_2.3.0 hgu133plus2.db_2.2.5 hgu133a2.db_2.2.5
[11] hgu133a2cdf_2.3.0 Harshlight_1.12.0
altcdfenvs_2.4.0 hypergraph_1.14.0 graph_1.20.0
[16] Biostrings_2.10.16 IRanges_1.0.12
makecdfenv_1.20.0 affyio_1.10.1 maCorrPlot_1.12.0
[21] lumiHumanIDMapping_1.0.1 lumi_1.8.3
mgcv_1.4-1.1 affyQCReport_1.20.0 RColorBrewer_1.0-2
[26] affyPLM_1.18.1 preprocessCore_1.4.0
simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1
[31] genefilter_1.22.0 survival_2.34-1
affy_1.20.2 lumiHumanAll.db_1.4.0 RSQLite_0.7-1
[36] DBI_0.2-4 beadarray_1.10.0
sma_0.5.15 hwriter_1.0 geneplotter_1.20.0
[41] annotate_1.20.1 xtable_1.5-4
AnnotationDbi_1.4.3 lattice_0.17-17 Biobase_2.2.2
[46] limma_2.16.4
loaded via a namespace (and not attached):
[1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21
XML_2.1-0 cluster_1.11.11 grid_2.8.1
