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

[Elliot Kleiman]

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_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_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/