[BioC] Illumina annotation problem - illuminaHumanv2GENENAME

McClellan, Elizabeth Ann eamcclel at mail.smu.edu
Mon Dec 15 23:41:07 CET 2008

Thank you! Problem solved. 

Elizabeth McClellan
Department of Statistical Science
Southern Methodist University
From: Lynn Amon [lamon at fhcrc.org]
Sent: Monday, December 15, 2008 4:28 PM
To: McClellan, Elizabeth Ann
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Illumina annotation problem - illuminaHumanv2GENENAME

Use illuminaHumanv2BeadID.db instead.  You might want to take the one
from the devel version instead of the release version as there were some
problems with the initial package.

McClellan, Elizabeth Ann wrote:
> 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
> Elizabeth McClellan
> Department of Statistical Science
> Southern Methodist University
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