[BioC] lumiHumanAll.db, Gostats

[Pan Du]

Hi Al,

The current version of lumiHumanAll.db was built based on Illumina Company
provided annotation files. As the probes were designed based on different
sources, lots of probes have no EntrezID available. One option is to blast
the probe sequence against the latest human genome to get the mappings. The
probe sequence can be easily converted from nuID by id2seq() function in the
lumi package. You can also check
https://prod.bioinformatics.northwestern.edu/nuID/
, which list the mapping between nuID and corresponding annotations. I am
trying to convert these mapping as annotation libraries within next two
months.


Pan


On 6/10/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Tue, 10 Jun 2008 06:40:19 +0100
> From: "Al Ivens" <alicat at sanger.ac.uk>
> Subject: [BioC] lumiHumanAll.db, GOstats
> To: "'bioc'" <bioconductor at stat.math.ethz.ch>
> Message-ID: <00ad01c8cabc$7b2e8d90$5ebcd781 at internal.sanger.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi,
> 
> Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After
> linear model fitting and clustering, I have identified a cluster of ~130
> loci that show an interesting profile.  However, as 125 of them have no
> GeneName or EntrezID, I am struggling to figure out what they might be
> biologically.  
> 
>> From a closer inspection of lumiHumanALl.db, I find that approx. half of
> the features have no EntrezID, so I wasn't just unlucky with the
> constituents of my cluster!
> 
> Does anyone have any recommendations as to the best approach to get
> around this problem (which came to light when I tried to run GOstats,
> which requires EntrezID for mapping of terms)?
> 
> Many thanks in advance.
> 
> Cheers,
> 
> a
> 
> 
> 
> 
> -- 
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------------------------------------------------------
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan at northwestern.edu