[BioC] Illumina annotation problem - illuminaHumanv2GENENAME

McClellan, Elizabeth Ann eamcclel at mail.smu.edu
Mon Dec 15 22:12:48 CET 2008

Dear Users,

I have summarized data from an Illumina Human-6 v2 array with IDs numbered "10008", "10010",,...,"7650767", "7650768", and I am trying to look at functions of or get some information about some of these genes.  I am using the illuminaHumanv2.db package and get a "NULL" output for any function that is supposed to take my probeset name as input, e.g. illuminaHumanv2GO[["10008"]] or illuminaHumanv2SYMBOL[["10008"]].  I have noticed that Illumina IDs such as "ILMN_1001" work properly with these functions, but I don't have such a prefix.  I still get nothing if I strip off the "ILMN_".  I visited Illumina's "Annotation Files Archive" with no avail.    Is there a way to get gene names, symbols, anything, with these types of IDs?

Here is my relevant session info:

R version 2.8.0 (2008-10-20)
other attached packages:
 [1] GOstats_2.8.0            Category_2.8.1
 [3] genefilter_1.22.0        survival_2.34-1
 [5] RBGL_1.18.0              annotate_1.20.1
 [7] xtable_1.5-3             graph_1.20.0
 [9] GO.db_2.2.5              illuminaHumanv2.db_1.1.3
[11] RSQLite_0.7-1            DBI_0.2-4
[13] AnnotationDbi_1.4.1      Biobase_2.2.1

Thank you,

Elizabeth McClellan
Department of Statistical Science
Southern Methodist University

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