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

Mark Dunning mark.dunning at gmail.com
Wed Mar 6 10:55:39 CET 2013

I tend to work with things on the probe-level too. I have seen many
example of genes where some probes target obscure transcripts or are
just badly-designed. By including them in the averaging, you would be
diluting the signal from the good probes.

Sometimes you have to collapse the data to one probe per-gene, and for
this I tend to pick the "best" probe for each gene by using a  measure
such as IQR across the dataset.

On Wed, Mar 6, 2013 at 1:52 AM, Ying Wu <daiyingw at gmail.com> wrote:
> 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.
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