[BioC] Definition of probes in lumiHumanAll annotation database

[Pan Du]

Hi Javier

The lumiHumanAll.db annotation package use nuID as probe ID, which is
a direct unique mapping of the Illumina probe sequence. You can use
"id2seq" function in lumi package to recover the probe sequence, and
"seq2id" function to convert back. Please check the paper "nuID: A
universal naming schema of oligonucleotides for Illumina, Affymetrix,
and other microarrays".(PMID 17540033) for more details.
 The mapping from nuID to RefSeq ID in lumiHumanAll.db was based on
the latest annotation provided by Illumina company. If you want to
further check potential multiple mappings to gene isoforms (I believe
the Illumina annotation should have removed the probes with multiple
mappings), you can check it based on the probe sequence.

Hope this is helpful to you.

Pan

> Date: Mon, 2 Apr 2012 09:47:39 +0200
> From: Javier P?rez Florido <jpflorido at gmail.com>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Definition of probes in lumiHumanAll annotation
>        database
> Message-ID: <4F79599B.50309 at gmail.com>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Dear list,
> I've checked all the annotation elements given by lumiHumanAll.db and,
> as far as I know, none of them provides the definition of probes. If I'm
> not wrong, this definition can distinguishes isoforms and other factors.
> How can I get such information from the lumiHumanAll annotation file?
> For example, gene A1CF has three different probes, corresponding each
> one to a different transcript variant, but I cannot obtain such
> information from the lumiHumanAll database.
>
> Thanks,
> Javier
>
>
>
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