[BioC] Newbie Illumina Probe Annotation (beadarray) Problem

[Lynn Amon]

One of the problems is that Illumina has changed the format of its
identifiers.   Perhaps the illuminaMousev1p1.db package should be
changed to use the "ILMN_" type identifiers.
Lynn Amon


Priscila Darakjian wrote:
> Actually, I would look at MouseRef-8_V1_1_R3_11234312_A.bgx (this probably has some annotation changes that were not present in R1)
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Priscila Darakjian
> Sent: Thursday, January 29, 2009 9:30 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Newbie Illumina Probe Annotation (beadarray) Problem
>
> 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)
> MouseRef-8_V1_1_R1_11234312_A.bgx
>
> Good luck,
>
> Priscila
>
>
> -----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.
> cheers
>
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>
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