[BioC] How to convert Illumina ProbeIDs to nuIDs without nuID indexed annotation libraries?

[Elliot Kleiman]

Hi Pan,

I was wondering, do you have a plan to release a nuID indexed
annotation mapping for the Rat for BioC release 2.3?
e.g., lumiRatIDMapping.db'

RE: I did not see an equivalent, 'lumiRatIDMapping.db' package on
the devel site for BioC 2.3 or am I wrong?
* http://www.bioconductor.org/packages/2.3/data/annotation/

Thank you,

... Elliot

Pan Du wrote:
> Hi Elliot,
>
> You can find the Illumina ID mapping packages, lumiHumanIDMapping.db and
> lumiMouseIDMapping.db, in the Bioc 2.3 (Developing). These packages include
> all types of Illumina IDs and corresponding nuIDs. To do ID mapping, you
> also need to update the lumi package to the developing version lumi 1.7.23.
> Please read the vignette "IlluminaAnnotation.pdf" before using them. All
> these packages can be installed and ran in R 2.7 or above. If you are using
> R 2.7, you need to manually download and install them,  biocLite cannot
> install developing version packages.
> Tell me if you have any questions.
>
>
> Pan
>
>
>
> On 9/23/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
> <bioconductor-request at stat.math.ethz.ch> wrote:
>
>   
>> Message: 3
>> Date: Tue, 23 Sep 2008 00:39:50 -0700
>> From: Elliot Kleiman <kleiman at rohan.sdsu.edu>
>> Subject: [BioC] How to convert Illumina ProbeIDs to nuIDs without nuID
>> indexed annotation libraries?
>> To: bioconductor at stat.math.ethz.ch
>> Message-ID: <48D89D46.2050405 at rohan.sdsu.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi BioC,
>>
>> [Question]:
>> * How do you convert Illumina ProbeIDs to nuIDs without nuID
>> indexed annotation libraries?
>>
>> i.e.,
>>
>> ... the following previous BioC 2.1 released nuID indexed annotation
>> libraries,
>>
>> * lumiRatV1
>> * lumiMouseV1
>> * lumiHumanV1
>> * lumiHumanV2
>>
>> ... are not available in BioC release 2.2,
>> * http://www.bioconductor.org/packages/2.2/data/annotation/
>>
>> RE: My objective is to map probeIDs to nuIDs standalone without
>> first having to create a lumiBatch object via the lumi package.
>>
>> There is a new annotation package, 'lumiRatAll.db' in BioC 2.2,
>> but it doesn't provide the functional mapping of ProbeIDs to nuIDs;
>> it assumes you already have nuIDs.
>>
>> e.g.,
>> The lumi package offers a function that can map Illumina probeIDs
>> to nuIDs, 'probeID2nuID()'. But the problem is that it requires
>> a 'lib' argument to specify a nuID indexed annotation library
>> (none of which are currently available in the current 2.2 release).
>> * http://www.bioconductor.org/packages/2.2/data/annotation/
>>
>> e.g.,
>>
>> # load lumi package from BioC release 2.2
>>     
>>> library(lumi)
>>>       
>> # get help on lumi function probeID2nuID
>>     
>>> help(probeID2nuID)
>>>       
>> Print-out excerpt of help documentation for function
>> 'probeID2nuID()' from package 'lumi',
>>
>> # probeID2nuID              package:lumi              R Documentation
>> # Usage:
>> # probeID2nuID(probeID, lib = "lumiHumanV1")
>> # Arguments:
>> # probeID: a vector of Illumina ProbeID
>> # lib: a nuID indexed Illumina annotation library
>>
>> e.g.
>> # Not Run b/c no annotation libs loaded b/c they aren't available to install
>>     
>>> nu <- probeID2nuID(pid, lib = "lumiHumanV1")
>>>       
>> Am I [like totally] missing something here?
>>
>> Thanks,
>>
>> ... Elliot
>>
>>     
>>> # print sessionInfo()
>>> sessionInfo()
>>>       
>> R version 2.7.2 (2008-08-25)
>> i686-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAG
>> ES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=e
>> n_US;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] illuminaRatv1ProbeID.db_1.1.1 GOstats_2.6.0
>>  [3] Category_2.6.0                genefilter_1.20.0
>>  [5] survival_2.34-1               RBGL_1.16.0
>>  [7] GO.db_2.2.0                   graph_1.18.1
>>  [9] lumiRatAll.db_1.2.0           lumi_1.6.2
>> [11] mgcv_1.4-1                    beadarray_1.8.0
>> [13] affy_1.18.2                   preprocessCore_1.2.1
>> [15] affyio_1.8.1                  geneplotter_1.18.0
>> [17] annotate_1.18.0               xtable_1.5-3
>> [19] AnnotationDbi_1.2.2           RSQLite_0.7-0
>> [21] DBI_0.2-4                     lattice_0.17-14
>> [23] Biobase_2.0.1                 limma_2.14.6
>>
>> loaded via a namespace (and not attached):
>> [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.11
>> grid_2.7.2       
>> [5] tcltk_2.7.2
>>
>> -- 
>> __________________________
>> MS graduate student
>> Program in Computational Science
>> San Diego State University
>> http://www.csrc.sdsu.edu/
>> http://www.rohan.sdsu.edu/~kleiman/
>>
>>     
>
>
>
>
>   


-- 
__________________________
MS graduate student 
Program in Computational Science 
San Diego State University
http://www.csrc.sdsu.edu/