[BioC] function error for "hyperGTest" in Category package

[Vincent Carey]

please read the posting guide.  you do not provide sessionInfo()
result nor a reproducible example.  if we take

entrezGeneIds = c("1000", "100")

we can find

> hyperGTest(params)
Gene to GO MF  test for over-representation
19 GO MF ids tested (6 have p < 0.01)
Selected gene set size: 2
    Gene universe size: 10785
    Annotation package: hgu133a

with sessionInfo:

> sessionInfo()
R version 2.10.0 Patched (2009-10-31 r50269)
i386-apple-darwin9.8.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
 [1] GO.db_2.3.5          GOstats_2.11.3       graph_1.23.7
 [4] Category_2.11.5      hgu133a.db_2.3.5     org.Hs.eg.db_2.3.6
 [7] RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.7.20
[10] Biobase_2.5.8        weaver_1.11.1        codetools_0.2-2
[13] digest_0.4.1

loaded via a namespace (and not attached):
[1] GSEABase_1.7.4    RBGL_1.21.14      XML_2.6-0         annotate_1.23.4
[5] genefilter_1.25.9 splines_2.10.0    survival_2.35-7   xtable_1.5-5


On Tue, Nov 3, 2009 at 4:43 AM, LIYUN <yli01 at sibs.ac.cn> wrote:
> Hi,
>
> I’m using the hypetGTest function to do gene enrichment analysis, but there
> shows errors like this:
>
> ”  invalid names for slots of class "GOHyperGResult": pvalues, oddsRatios,
> expectedCounts, catToGeneId”
>
>
>
> The code I’m using is :
>
> Ø   params <- new("GOHyperGParams", geneIds = entrezGeneIds,universeGeneIds
> = NULL, annotation ='hgu133a.db',ontology='MF')  #where entrezGeneIds is a
> vector of gene probe names.
>
> Ø  hyperGTest(params)
>
>
>
> all the packages and R version is updated to the latest version. I used to
> used this function in R 2.4.X and the low version of category , and it
> works. But when I used the updated version, it goes wrong.
>
>
>
> Any advise?
>
>
>
> Yun
>
>
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>
>
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