Fetching Illumina probe ID information

Check which annotation package you need for your microarray data at http://www.bioconductor.org/packages/release/data/annotation/

The results I’m looking at are from a Illumina HumanHT12v3 BeadChip microarray (illuminaHumanv3.db).

Make sure you’re running the latest version of R (R version 2.13.0 (2011-04-13)) and Bioconductor (Bioconductor version 2.8).

source("http://bioconductor.org/biocLite.R")
biocLite("illuminaHumanv3.db")
library("illuminaHumanv3.db")
ids = c("ILMN_1762337", "ILMN_2055271", "ILMN_1736007", "ILMN_2383229", "ILMN_1806310")
mget(ids, illuminaHumanv3GENOMICLOCATION)
#$ILMN_1762337
#[1] "chr7:20180663:20180712:-"
#
#$ILMN_2055271
#[1] "chr19:58856730:58856779:-"
#
#$ILMN_1736007
#[1] "chr19:58857369:58857418:-"
#
#$ILMN_2383229
#[1] "chr10:52566587:52566636:-"
#
#$ILMN_1806310
#[1] "chr10:52566496:52566545:-"

mget(ids, illuminaHumanv3PROBESEQUENCE)
#$ILMN_1762337
#[1] "GTGTTACAAGACCTTCAGTCAGCTTTGGACAGAATGAAAAACCCTGTGAC"
#
#$ILMN_2055271
#[1] "GGGATTACAGGGGTGAGCCACCACGCCCAGCCCCAGCTTAGTTTTTTAAA"
#
#$ILMN_1736007
#[1] "GCAGAGCTGGACGCTGTGGAAATGGCTGGATTCCTCTGTGTTCTTTCCCA"
#
#$ILMN_2383229
#[1] "TGCTGTCCCTAATGCAACTGCACCCGTGTCTGCAGCCCAGCTCAAGCAAG"
#
#$ILMN_1806310
#[1] "GAGGTCTACCCAACTTTTGCAGTGACTGCCCGAGGGGATGGATATGGCAC"
mget(ids, illuminaHumanv3GENENAME)
#$ILMN_1762337
#[1] "metastasis associated in colon cancer 1"
#
#$ILMN_2055271
#[1] NA
#
#$ILMN_1736007
#[1] NA
#
#$ILMN_2383229
#[1] "APOBEC1 complementation factor"
#
#$ILMN_1806310
#[1] "APOBEC1 complementation factor"

Sourced from Bioconductor mailing list thread -> [BioC] [Fwd: help in annotation ILLUMINA probes]

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