[BioC] About Illumina annotation IDENTIFIERS

Lynn Amon lamon at fhcrc.org
Sun May 25 22:22:25 CEST 2008

Hi Yang,
Illumina keeps changing their naming schemes for the probes so it was 
getting tricky using those as the identifiers.  BeadArray switched to 
ProbeIDs and it seemed like most people (including myself) were using 
those so I switched.  You do not need to use the existing platforms in 
GEO.  You just need to include an extra platform file when you submit 
which includes the ProbeID and one or two annotation columns.  You could 
use the accession identifier and gene symbol for those.   Check out



Sean Davis wrote:
> On Sun, May 25, 2008 at 9:46 AM, YANG Ling <ling.yang at picb.ac.cn> wrote:
>> Hi, Lynn,
>> I downloaded the illuminaHumanv2ProbeID.db package and want to plot some
>> genes on chromosomes. But the identifiers used in this packages are not the
>> same with the annotation file provided by GEO database. The latter use
>> TARGET ID(ex, GI-****).
>> Could you please tell me what are the identifiers preferred in the
>>  illuminaHumanv2ProbeID.db package? And HOW could I change those TARGET ID
>> used by GEO database to the most easily-used ones for
>>  illuminaHumanv2ProbeID.db?
> The package uses ProbeID rather than target ID.  What GEO accession
> are you trying to access?  The probe ID might or might not be in the
> GEO platform file.
> Sean
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