Excelent news... (I  noticed that there is an 'org.At.tair.db' also
available in the devel version!)
Thanks Herve for the info
A./

PS: I am still curious about the locking/unlocking issue...



2009/10/1 Hervé Pagès <hpages@fhcrc.org>

> Forgot to send my sessionInfo(), sorry:
>
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-24 r49817)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu95av2.db_2.3.5    org.Hs.eg.db_2.3.5   genefilter_1.25.9
> [4] ath1121501.db_2.3.5  org.At.tair.db_2.3.5 RSQLite_0.7-2
> [7] DBI_0.2-4            AnnotationDbi_1.7.17 Biobase_2.5.8
>
> loaded via a namespace (and not attached):
> [1] annotate_1.23.4 splines_2.10.0  survival_2.35-7 tools_2.10.0
> [5] xtable_1.5-5
>
>
> H.
>
>
>
> Hervé Pagès wrote:
>
>> Hi Ariel,
>>
>> One solution is that you use the development version of Bioconductor
>> (BioC 2.5, to be released soon, based on the R-2.10 series).
>>
>> In the development version of genefilter it looks like the nsFilter()
>> function has been improved in order to deal properly with the
>> peculiarity of the ath1121501.db package. Internally it's now
>> calling a little helper function .findCentralID() (not exported)
>> in order to determine what's the central ID in the annotation
>> package:
>>
>>  library(genefilter)
>>  library(hgu95av2.db)
>>  library(ath1121501.db)
>>  > genefilter:::.findCentralID("hgu95av2")
>>  [1] "ENTREZID"
>>  > genefilter:::.findCentralID("ath1121501")
>>  [1] "ACCNUM"
>>
>> Cheers,
>> H.
>>
>>
>> Ariel Chernomoretz wrote:
>>
>>> Hi all,
>>> I am currently analyzing some arabidopsis thaliana experiments
>>> (ath1121501
>>> GeneChip)
>>> The corresponding annotation package, ath1121501.db, is a little bit
>>> 'special' as
>>> there is no ENTREZID map for the chip.
>>> I would like to cheat and create  a fake ath1121501ENTREZID for the
>>> environment as a copied instance of ath1121501ACCNUM (in order to use,
>>> for
>>> instance,  the genefilter package's function "nsFilter" to deal with non
>>> annotated, or duplicated probesets)
>>>
>>> The problem is that I am not able to create a new entry in the
>>> package:ath112150.db as it is a locked environment. Is there any way to
>>> temporarily unlock it, do some stuff and lock it again?
>>> (It seems easy to lock environments, using the lockEnvironment function,
>>> but
>>> I did not find an easy way to unlock them)
>>>
>>> Thanks in advance
>>> Ariel./
>>>
>>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Dr. Ariel Chernomoretz
      Departamento de Fisica, FCEyN,        Universidad de Buenos Aires,
      (1428) Ciudad Universitaria,        Ciudad de Buenos Aires, Argentina.
      TE +54 11 4576 3390 ext 817
      Fax +54 11 4576 3357
      email: ariel@df.uba.ar        Webpage:
http://www.df.uba.ar/users/ariel

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