
Hi, Sean, 
I see your point. Could you please tell me how I can access the "company-supplied annotation"? 
Thanks.
Lingsheng 



> Date: Fri, 14 Mar 2008 20:39:49 -0400
> From: sdavis2@mail.nih.gov
> To: dong_lsh@hotmail.com
> Subject: Re: [BioC] CodeLink Probe ID in new Annoation Package different from the NCBI GEO?
> CC: bioconductor@stat.math.ethz.ch
> 
> On Fri, Mar 14, 2008 at 8:25 PM, Lingsheng Dong <dong_lsh@hotmail.com> wrote:
> >
> >  Hi, Sean,
> > Thank you very much for you response.  I understand your point.
> > But the question we are trying to ask is this:
> > Because the Array was designed years ago, part of the old annotation
> > (GPL1449) should be out of date. If we map the probe sequences to most
> > updated RefSeq RNA database and re-analyze the data, we may find some more
> > interesting genes. So we don't want use any data from the old annotation
> > (GPL1449). In the annotation package h20kcod, probe ID is different from the
> > original platform and the expression table. So there is noway to use the
> > package.
> > If there is not an answer to this problem, could you please tell how I can
> > download the probe sequences with the original probe ID?
> 
> The bioconductor annotation packages are generally built using
> company-supplied annotation; that may have changed, but very well
> might not have.  In other words, if the company says that a probe
> mapped to NM_000022, then the bioconductor annotation package uses
> that RefSeq accession for further lookups.  Generally, no attempt is
> made to realign the probes to the newest build of refseq.
> Unfortunately, I do not know if you can find or where to find the
> probe sequences and original probe IDs.
> 
> Sean

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