[BioC] how to annotate Illumina HumanHT-12 v3 chips?
daiyingw at gmail.com
Wed Mar 6 02:52:20 CET 2013
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
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:
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?
> <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
> 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
> 2) If different kinds of probes (such as RefSeq NM and RefSeq XM) are
> mapped to the same gene, how to combine them?
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