[BioC] illumina annotation packages vs. bgx manifests

[Lynn Amon]

Hi Michal,
I'm not completely certain what you are asking.  The Array_Address_ID is 
the probe identifier used in the illuminaRatv1ProbeID.db annotation 
package so you should link using that identifier.  If you are going to 
use the .bgx file for annotation, you don't really need an annotation 
package at all. 
Lynn


Michal Kolář wrote:
> Dear List,
>
> I wonder what is the correct probe identifier for illumina annotation 
> packages.
>
> 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 differences.
>
> Cheers,
> Michal
>
>
> -- 
> -----------------------------------------------------
> 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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