[BioC] problem with GO terms

Mon Nov 28 23:32:20 CET 2011

Hi Ina,

It would be helpful if you would give us a _minimal_  and functional 
example of what you did. We will also need the set of entrez IDs you 
used in order to see if we can duplicate. You can output your entrez IDs 
using the dump() function (e.g., dump("entrezIDs", "")).

Best,

Jim

On 11/28/2011 5:08 PM, Ina Hoeschele wrote:
> Hi all,
>    I am sorry but I still have not been able to solve my problem. I did a GO analysis using GOstats on another dataset, this time a canine dataset. The top BP category that I get from GOstats again does not exist any more! Please see below. I reinstalled everything, including GOstats, and have the current versions. How is it possible for GOstats to give me these old categories ...
>
>> get("GO:0035637",canine2GO2PROBE)
> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
>    value for "GO:0035637" not found
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] org.Hs.eg.db_2.6.4   GOstats_2.20.0       graph_1.32.0
>   [4] Category_2.20.0      KEGG.db_2.6.1        GO.db_2.6.1
>   [7] biomaRt_2.10.0       canine2cdf_2.9.1     canine2.db_2.6.3
> [10] org.Cf.eg.db_2.6.4   RSQLite_0.10.0       DBI_0.2-5
> [13] annotate_1.32.0      AnnotationDbi_1.16.5 limma_3.10.0
> [16] made4_1.28.0         scatterplot3d_0.3-33 gplots_2.10.1
> [19] KernSmooth_2.23-7    caTools_1.12         bitops_1.0-4.1
> [22] gdata_2.8.2          gtools_2.6.2         RColorBrewer_1.0-5
> [25] ade4_1.4-17          affy_1.32.0          Biobase_2.14.0
> [28] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         genefilter_1.36.0     GSEABase_1.16.0
>   [4] IRanges_1.12.3        preprocessCore_1.16.0 RBGL_1.30.1
>   [7] RCurl_1.7-0.1         splines_2.14.0        survival_2.36-10
> [10] tools_2.14.0          XML_3.4-3             xtable_1.6-0
> [13] zlibbioc_1.0.0
>
> ----- Original Message -----
> From: "James W. MacDonald"<jmacdon at med.umich.edu>
> To: "Ina Hoeschele"<inah at vbi.vt.edu>
> Cc: "Bioconductor mailing list"<bioconductor at r-project.org>
> Sent: Tuesday, November 22, 2011 1:52:56 PM
> Subject: Re: [BioC] problem with GO terms
>
> Hi Ina,
>
>
>
> On 11/22/2011 1:03 PM, Ina Hoeschele wrote:
>> thank you, Jim ...
>> I did what you show below and I get the same result:
>>
>>    >   get("GO:0050864", org.Hs.egGO2EG)
>> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
>>      value for "GO:0050864" not found
>>
>> but why is GOstats giving me this GO term?
> Did you use GOstats with this current version of BioC, or are you using
> data you processed sometime in the past?
>
> As far as I can tell, it is impossible for you to be getting that GO
> term if you are using the current version of these packages. I am
> assuming that your data are from the Illumina Human V4 chip.
>
>   >  get("GO:0050864", illuminaHumanv4GO2PROBE)
> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
>     value for "GO:0050864" not found
>
> This is with the version of the illuminaHumanV4.db package that you are
> using. Since this isn't even in that package, it is not possible for
> GOstats to be reporting it as being significant.
>
> Best,
>
> Jim
>> Thanks again, Ina
>>
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>    [1] biomaRt_2.10.0            GOstats_2.20.0
>>    [3] graph_1.32.0              Category_2.20.0
>>    [5] PFAM.db_2.6.1             KEGG.db_2.6.1
>>    [7] GO.db_2.6.1               annotate_1.32.0
>>    [9] illuminaHumanv4.db_1.12.1 org.Hs.eg.db_2.6.4
>> [11] RSQLite_0.10.0            DBI_0.2-5
>> [13] AnnotationDbi_1.16.4      Biobase_2.14.0
>> [15] BiocInstaller_1.2.1
>>
>> loaded via a namespace (and not attached):
>>    [1] genefilter_1.36.0 GSEABase_1.16.0   IRanges_1.12.2    RBGL_1.30.1
>>    [5] RCurl_1.7-0.1     splines_2.14.0    survival_2.36-10  tools_2.14.0
>>    [9] XML_3.4-2.2       xtable_1.6-0

-- 
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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