This works great. Thank you everyone for your input. Pete On Wed, Jul 28, 2010 at 7:55 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > 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 >> > >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]]