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

[James MacDonald]

Hi Jenny,

You want multiassign() in Biobase.

Something like this should do the trick:

tmp  <- eapply(ath1121501MULTIHIT,
	function(ids) if(length(ids) >1) "multiple" else ids)
ath112150ACCNUM <- new.env(hash=TRUE, parent=.GlobalEnv)
multiassign(tmp, envir=ath112150ACCNUM)

Best,

Jim



Jenny Drnevich wrote:
> Hi Herve,
> 
> Thanks for looking into this. Unfortunately, your fix didn't quite work:
> 
> 
>> You can compute the ath1121501ACCNUM yourself with:
>>
>>> ath1121501ACCNUM <- eapply(ath1121501MULTIHIT,
>>                              function(ids) if (length(ids) > 1) 
>> "multiple" else ids)
> 
> This changes ath1121501ACCNUM from an environment to a list, and to 
> use hyperGTest(), it needs to be an environment. I know very little 
> about environments, and the simple as.environment() didn't work, so I 
> don't know how to fix it.
> 
> Thanks,
> Jenny
> 
> 
> 
>> Let me know if you find any other problem.
>>
>> Thanks!
>> H.
>>
>>
>>> 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
> 
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623