[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[Robert Gentleman]

Hi Jenny,
   We will have a look and see if something obvious has gone wrong...
any arabadopsis experts that might know something more should feel free 
to venture an opinion here...


Jenny Drnevich wrote:
> Hi Herve,
> 
> Thanks for letting me know the new Windows binaries were available. 
> However, I traced the problem to the new annotation package for 
> ath1121501 - it is USELESS for GOstats testing!! Arabidopsis doesn't use 
> EntrezIDs, but instead uses AGI locus identifier, given in the 
> ath1121501ACCNUM environment. This environment used to give unique IDs 
> for almost all probe sets, but now all of the listings are either 
> "multiple" or NA:
> 
>  > probes <- ls(ath1121501ACCNUM)
>  > probes[1:10]
>  [1] "244901_at"   "244902_at"   "244903_at"   "244904_at"   "244905_at"
>  [6] "244906_at"   "244907_at"   "244908_at"   "244909_at"   "244910_s_at"
>  > length(probes)
> [1] 22810
>  > locusList <- unique(unlist(mget(probes, ath1121501ACCNUM)))
>  > length(locusList)
> [1] 2
>  > locusList
> [1] "multiple" NA
> 
> 
> I realize this is probably came from the Arabidopsis database used to 
> create the annotation package, but is there any way to "fix" this, or to 
> put up the older annotation package?  The old one had a few hundred 
> "multiple" entries, but I figured it wouldn't matter that much to throw 
> them out. Any other ideas for ways around this problem?
> 
> Thanks,
> Jenny
> 
>  > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
> 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] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>  [1] limma_2.11.13        ath1121501_1.99.10   GOstats_2.3.17
>  [4] Category_2.3.39      genefilter_1.15.11   survival_2.32
>  [7] RBGL_1.13.6          annotate_1.15.11     xtable_1.5-1
> [10] GO.db_1.99.3         AnnotationDbi_0.99.1 RSQLite_0.6-2
> [13] DBI_0.2-3            graph_1.15.20        Biobase_1.15.34
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.7     simpleaffy_2.13.01
> 
> 
> 
> 
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org