[BioC] how to annotate Illumina HumanHT-12 v3 chips?

[Ying Wu]

The answer depends on what you are interested in biologically. If you 
are only interested in well-annotated coding genes for downstream 
pathway analysis, then only use the NM_ genes.

Is there a reason why you want to combine the probes for each gene? Some 
software that I've used has used median/mean to collapse multiple probes 
signals into one gene but I found it useful to work with things on the 
probe level.

As a sidenote, there is a bioconductor package that has Illumina 
annotations that might be better than the ones the manufacture provides 
and it can be found here: 
http://www.bioconductor.org/packages/2.11/data/annotation/html/illuminaHumanv3.db.html

Best,
Ying

On 3/4/2013 3:00 AM, bioconductor-request at r-project.org wrote:
> Message: 3
> Date: Sun, 3 Mar 2013 16:30:30 -0500
> From: Feng Tian <fengtian at bu.edu>
> To: bioconductor at r-project.org
> Subject: [BioC] how to annotate Illumina HumanHT-12 v3 chips?
> Message-ID:
> 	<CALimmDjDzoQ_11CC4qBhRSPAaZFdL6rdu_BPbtn9YrnyFdDNEA at mail.gmail.com>
> Content-Type: text/plain
>
> Hi all list,
>
> I want to annotate Illumina HumanHT-12 v3 chips by using the annotation
> file download from Illumina.
> The Illumina probes are classified by
>
> RefSeq
> NM            Coding transcript, well-established annotation
> XM            Coding transcript, provisional annotation
> NR            Non-coding transcript, well-established annotation
> XR            Non-coding transcript, provisional annotation
>
> Supplementary Content
> UniGene (Build 199) Experimentally confirmed mRNA sequences that align to
> EST clusters.
>
> I have the following questions
> 1) Should I use all kinds of these probes? Should I only use the RefSeq NM
> probes?
>
> 2) If different kinds of probes (such as RefSeq NM and RefSeq XM) are
> mapped to the same gene, how to combine them?
>
> Thanks.