[BioC] illumina annotation packages vs. bgx manifests

Michal Kolář kolarmi at img.cas.cz
Tue Jul 22 15:29:24 CEST 2008

Dear List,

I wonder what is the correct probe identifier for illumina annotation  

I have the illumina raw data (tiff) where the beads are identified by  
their corresponding Array_Address_ID, and then I have the illumina  
manifest file (.bgx). I use the illuminaRatv1 annotation package. And  
my question is, how can I map Array_Address_IDs to the identifiers of  
the annotation package.

I read in several postings in the List, that these identifiers should  
be the TargetIDs in the manuscript. But there is no TargetID in the  
rat manuscript (.bgx). There are however two other identifiers that  
look similar to the identifiers of the annotation package. One of  
them is Probe_ID, but there is no overlap between the two IDs sets.  
The other is called Transcript and that one looks better, but still  
only one third of the identifiers matches. So what is the correct  
column in the manifest to link against? (If any.)

I know I can use the illuminaRatv1ProbeID.db package to link directly  
against Array_Address_ID or lumiRatV1 to link against probe  
sequences, but I want to compare the packages and to see possible  


Michal Kolář

Academy of Sciences of the Czech Republic
Institute of Molecular Genetics
Vídeňská 1083
CZ-14220 Praha
Czech Republic

phone:	+420 296 443 412
email:	kolarmi at img.cas.cz
www:  	http://www.thp.uni-koeln.de/~kolarmi/research

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