What about lumiHumanIDMapping?  In conjunction with lumi, you can get probe
sequences corresponding to any identifier for any
of the listed human chip versions:

> con = lumiHumanIDMapping_dbconn()
> dbListTables(con)
 [1] "HumanHT12_V3_0_R1_11283641_A" "HumanHT12_V3_0_R2_11283641_A"
 [3] "HumanRef8_V2_0_R1_11223162_A" "HumanRef8_V2_0_R2_11223162_A"
 [5] "HumanRef8_V3_0_R0_11282963_A" "HumanRef8_V3_0_R1_11282963_A"
 [7] "HumanRef8_V3_0_R2_11282963_A" "HumanWG6_V1"
 [9] "HumanWG6_V2_0_R1_11223189_A"  "HumanWG6_V2_0_R2_11223189_A"
[11] "HumanWG6_V2_11223189_B"       "HumanWG6_V3_0_R0_11282955_A"
[13] "metadata"                     "nuID_MappingInfo"
> dbGetQuery(con, "select * from HumanWG6_V1 limit 5")
    Search_key        Target    ProbeId   Accession Symbol
nuID
1        PLAC3 GI_23097300-A 0002360044 NM_021936.1  PLAC3
cn0dn1Sqdb0UHE4nEY
2         COG4 GI_21070955-A 0003940446 NM_015386.1   COG4
iklSlJ.eTo60t35XQE
3 GI_4505876-A  GI_4505876-A 0006420736 NM_000445.1  PLEC1
NBHBeFupql_azWVUMA
4        PTPRD GI_18860893-A 0002630279 NM_130393.1  PTPRD
KcSlfQzU6Ld94lMSpE
5       HS6ST2 GI_27597081-A 0003120162 NM_147174.2 HS6ST2
ZeMrPvoCSjgl4lLoAk
> id2seq(.Last.value$nuID)
                                  cn0dn1Sqdb0UHE4nEY
"GCTTCACTCGCTTCCCAGGGGCTCCGTTCACCAACTACATGAGCTACACG"
                                  iklSlJ.eTo60t35XQE
"GCAGCCCAGGCCAGCTTTCTGCATGGATGGTCAGTCTCTTGCCCTCAAAC"
                                  NBHBeFupql_azWVUMA
"AACACTAACCTGACCGTGGGCGGGGCCTTGCGGTATCCGCCCCCAATAAA"
                                  KcSlfQzU6Ld94lMSpE
"CTACAGGCCCTTCAATATCCATGGAGTCTCTTCTGAGCCATACAGGGCAC"
                                  ZeMrPvoCSjgl4lLoAk
"CTGATAGGTATTGTTGGAAAGCAGGATGAAGCCTGAGCCAGTGGAAAAGC"


On Wed, Jul 28, 2010 at 3:30 AM, Groot, Philip de <philip.degroot@wur.nl>wrote:

> Hello all,
>
> No, probe libraries for Illumina are not available. They should not be
> because you can export the probe sequences in beadstudio. Exporting those is
> really helpful in properly analysing illumina arrays in the lumi package!
>
> Probe sequences can be found on the Illumina annotation files on their
> website:
> http://www.illumina.com/support/annotation_files.ilmn
>
> Note that the lumi function "addNuID2lumi" contains the option
> "annotationFile=" that should point to the proper annotation file as listed
> above. This way, it is possible to obtain NuIDs because the probe sequences
> are available.
>
> I hope that this information helps a bit.
>
> Regards,
>
> Dr. Philip de Groot Ph.D.
> Bioinformatics Researcher
>
> Wageningen University / TIFN
> Nutrigenomics Consortium
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA  Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail:   Philip.deGroot@wur.nl
> Internet: http://www.nutrigenomicsconsortium.nl
>             http://humannutrition.wur.nl/
>             https://madmax.bioinformatics.nl/
> ________________________________________
> From: Mike Smith [grimbough@googlemail.com]
> Sent: 28 July 2010 11:24
> To: Peter Bazeley
> Cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] Illumina chip probe sequences
>
> Hi Pete,
>
> I'm not sure if there are any packages which provide the probe
> sequences, but the annotation files provided by Mark Dunning are based
> on the files found here :
> http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html
>
> The files have rather a lot of information  in them, but you can dig out
> the probe sequences for most of the human and mouse expression arrays.
>
> I hope that's some help,
>
> Mike Smith
>
> Peter Bazeley wrote:
> > Dear List,
> >
> > Is there a package that stores the probe sequences for Illumina's chips,
> > sort of like the hgu133aprobe package?
> >
> >
> > Thank you for any input,
> > Pete
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
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>

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