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

[Vincent Carey]

Please keep the dialogue on the mailing list.  The maintainers of the
package may comment on this phenomenon.

On Tue, Nov 3, 2009 at 11:46 PM, LIYUN <yli01 at sibs.ac.cn> wrote:
> Thank you very much for your help, the problem has been solved. It turns out that the problem is arise because of some sequence difference of loading these packages, but I'm not sure where the problem is. You may try load the package and run the functions in the following sequence:
> ###########
>        library( GO.db)
>        library(Category)
>        library(hgu133a.db)
>        library(GOstats)
>        params <- new("GOHyperGParams", geneIds = c('1000','100'),universeGeneIds = NULL, annotation ='hgu133a.db',ontology='MF')
>        hyperGTest(params)
> ############
> It will return a correct result.
>
> Now you close the R ,and restart an new R, and if this time you miss to load (GOstats) at the first time:
> ########
>        library( GO.db)
>        library(Category)
>        library(hgu133a.db)
>        params <- new("GOHyperGParams", geneIds = c('1000','100'),universeGeneIds = NULL, annotation ='hgu133a.db',ontology='MF')
>        hyperGTest(params)
> ########
> It will report the following error:
> ########
>        error: getClass(Class, where = topenv(parent.frame())) :
>        c("\"GOHyperGResult\" is not a defined class", "\"MFHyperGResult\" is not a defined class")
> ########
> But when you load GOstats after seeing this error messages:
> ########
>        library(GOstats)
>        params <- new("GOHyperGParams", geneIds = c('1000','100'),universeGeneIds = NULL, annotation ='hgu133a.db',ontology='MF')
>        hyperGTest(params)
> ########
> It still report an error like this:
> ########
>        Error: initialize(value, ...) :
>         invalid names for slots of class "GOHyperGResult": pvalues, oddsRatios, expectedCounts, catToGeneId, organism
> ########
>
> I'm confused about this problem. SessionInfo for both is the same.
>
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Chinese_People's Republic of China.936  LC_CTYPE=Chinese_People's Republic of China.936
> [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C
> [5] LC_TIME=Chinese_People's Republic of China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] GOstats_2.12.0      graph_1.22.2        hgu133a.db_2.3.5    org.Hs.eg.db_2.3.6  Category_2.12.0     GO.db_2.3.5
>  [7] RSQLite_0.7-3       DBI_0.2-4           AnnotationDbi_1.8.0 Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.24.0   genefilter_1.28.0 GSEABase_1.8.0    RBGL_1.20.0       splines_2.10.0    survival_2.35-7
> [7] tools_2.10.0      XML_2.6-0         xtable_1.5-5
>>
>
>
>
>
> ----Original Message-----
> From: Vincent Carey [mailto:stvjc at channing.harvard.edu]
> Sent: 2009年11月3日 18:27
> To: LIYUN
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] function error for "hyperGTest" in Category package
>
> 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
>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus signature database 4522 (20091019) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus signature database 4522 (20091019) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
>
>