[BioC] CodeLink Probe ID in new Annoation Package different from the NCBI GEO?

Diego Diez diez at kuicr.kyoto-u.ac.jp
Sat Mar 15 03:06:40 CET 2008

Hi Lingsheng,

I maintain the codelink annotation packages in the Bioconductor
project. The probe id you mention corresponds according to the
manufacturer to LEGACY_PROBE_NAME, i.e. probably was use as an initial
probe id some time ago. The probe ids are those listed as GExxxx. You
need to remap the legacy probe ids to the official probe ids in order
to use the annotation packages. Unfortunately since the Codelink
platform has changed from GE Healthcare to Applied microarrays, they
don't provide the gene list files anymore and the old ones are no
longer available in the web. I use the last version of these files to
generate the annotation packages- If I send you this files (offline)
you could do the remapping. A long term approach could be to add that
information into the annotation packages itself. I don't know how
feasible is that right now.

As for Sean comment, the last time that GE made a remap of the
codelink probes was on March 2006. Therefore the mapping is quite old
and I am sure that some probes will benefit of a new remap. So far I
am trusting the old mapping when analyzing codelink data. No idea if
Applied will make the information about Codelink arrays public again
or if they plan to remap the probes.



On Sat, Mar 15, 2008 at 10:15 AM, Lingsheng Dong <dong_lsh at hotmail.com> wrote:
>  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 at mail.nih.gov
>  > To: dong_lsh at hotmail.com
>  > Subject: Re: [BioC] CodeLink Probe ID in new Annoation Package different from the NCBI GEO?
>  > CC: bioconductor at stat.math.ethz.ch
> >
>  > On Fri, Mar 14, 2008 at 8:25 PM, Lingsheng Dong <dong_lsh at 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 (GPL1449) should be out of date.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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Dr. Diego Diez
Bioinformatics center,
Institute for Chemical Research,
Kyoto University.
Gokasho, Uji, Kyoto 611-0011 JAPAN
diez at kuicr.kyoto-u.ac.jp

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