[BioC] Illumina chip probe sequences

[Groot, Philip de]

Hello all,

No, probe libraries for Illumina are not available. They should not be because you can export the probe sequences in beadstudio. Exporting those is really helpful in properly analysing illumina arrays in the lumi package!

Probe sequences can be found on the Illumina annotation files on their website:
http://www.illumina.com/support/annotation_files.ilmn

Note that the lumi function "addNuID2lumi" contains the option "annotationFile=" that should point to the proper annotation file as listed above. This way, it is possible to obtain NuIDs because the probe sequences are available.

I hope that this information helps a bit.

Regards,

Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl
Internet: http://www.nutrigenomicsconsortium.nl
             http://humannutrition.wur.nl/
             https://madmax.bioinformatics.nl/
________________________________________
From: Mike Smith [grimbough at googlemail.com]
Sent: 28 July 2010 11:24
To: Peter Bazeley
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Illumina chip probe sequences

Hi Pete,

I'm not sure if there are any packages which provide the probe
sequences, but the annotation files provided by Mark Dunning are based
on the files found here :
http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html

The files have rather a lot of information  in them, but you can dig out
the probe sequences for most of the human and mouse expression arrays.

I hope that's some help,

Mike Smith

Peter Bazeley wrote:
> Dear List,
>
> Is there a package that stores the probe sequences for Illumina's chips,
> sort of like the hgu133aprobe package?
>
>
> Thank you for any input,
> Pete
>
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