[BioC] Newbie Illumina Probe Annotation (beadarray) Problem

Priscila Darakjian darakjia at ohsu.edu
Thu Jan 29 18:29:57 CET 2009

Look at http://www.switchtoi.com/annotationprevfiles.ilmn
I believe you will be interested specifically in either of these two files:
MouseRef-8_V1_1_R3_11234312_A.bgx (this is revision 3)

Good luck,


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of LeeH
Sent: Wednesday, January 28, 2009 2:50 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem

Hi all, I've been given an illumina dataset to process and have hit a bit of
a stumbling block adding in probe annotation using beadarray. The chip used
was the Illumina mouseRef-8 v1.1 expression beadchip. However, all i have is
the summary level data, annotated with probeids of the form "ILMN_nnnnnn" &
thats it. I've read as much documentation as i can get my hands on but still
havent managed to add in annotations, such as refseq IDs etc. I've
downloaded the various dbs and run annotations but all i get is the default
of NA.I looked into the probe tables using dbGetQuery and couldnt see
anywhere that i could map to ILMN_ ID's but I've never used this before & so
could well be missing something.

If anyone could point me in the direction it would be incredibly helpful.

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