Entering edit mode
James MacDonald <jmacdon at="" med.umich.edu=""> writes:
> 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)
or l2e ('list to environment'; also from Biobase).
> ath112150ACCNUM <- l2e(tmp)
Probably in Jim's use it makes sense to have parent=emptyenv(),
otherwise you can 'get' symbols that are defined in the global
environment rather than the environment you're looking in.
> x <- 1
> safer <- new.env(parent=emptyenv())
> unsafe <- new.env(parent=.GlobalEnv)
> get("x", safer)
Error in get("x", safer) : variable "x" was not found
> get("x", unsafe) # look in 'parent', i.e., .GlobalEnv
[1] 1
> get("l2e", unsafe) # parents of .GlobalEnv include the search() path
function (vals, envir)
{
if (missing(envir))
envir <- new.env(hash = TRUE, parent = emptyenv(), size =
.new_env_size(length(vals)))
.Call("listToEnv", vals, envir, PACKAGE = "Biobase")
}
<environment: namespace:biobase="">
Martin
> 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
>>
>> _______________________________________________
>> 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
>
> --
> 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
>
> _______________________________________________
> 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
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
