[BioC] lumiHumanAll.db, Gostats

[Al Ivens]

Hi Pan,

Thanks for your response, had a feeling BLAST was going to be the
answer!  I'll have a look at the web site first though.

Cheers,

a

> -----Original Message-----
> From: Pan Du [mailto:dupan at northwestern.edu] 
> Sent: 10 June 2008 16:11
> To: bioconductor at stat.math.ethz.ch; alicat at sanger.ac.uk
> Subject: Re: [BioC] lumiHumanAll.db, Gostats
> 
> 
> 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
> > 
> > 
> > 
> > 
> > --
> >  The Wellcome Trust Sanger Institute is operated by Genome Research
> >  Limited, a charity registered in England with number 1021457 and a
> >  company registered in England with number 2742969, whose registered
> >  office is 215 Euston Road, London, NW1 2BE.
> 
> 
> ------------------------------------------------------
> 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
> ------------------------------------------------------
>  
> 
> 
> 
> 




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.