[BioC] illumina annotation packages vs. bgx manifests

Pan Du dupan at northwestern.edu
Wed Jul 23 17:08:49 CEST 2008

Hi Michal,

The Illumina identifiers are always a confused issue. It completely changed
from version 1 to version 2 for Human and Mouse expression chips. Also it
has different types of identifiers. In order to simplify the issue, we have
created the Illumina ID mapping packages lumiHumanIDMapping.db and
lumiMouseIDMapping.db for Human and Mouse, respectively. (We will create the
Rat ID mapping package very soon.) These packages basically include all
types of identifiers included in previously released Illumina manifest files
of expression chips. There is "getChipInfo" and related functions in lumi
package (developing version) for ID conversion and retrieve chip
information. Please check the IlluminaAnnotation.pdf (More details will be
added to the vignette very soon) at
I will have a Lab session talking about Illumina ID mapping and annotation
at Bioc2008 next week. You can find more detailed information after the
meeting (or at the meeting if you attend the Bio2008). Thanks.


On 7/23/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 1
> Date: Tue, 22 Jul 2008 15:29:24 +0200
> From: Michal Kol?? <kolarmi at img.cas.cz>
> Subject: [BioC] illumina annotation packages vs. bgx manifests
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <27A717C2-EE28-4DE5-92E2-45495942B487 at img.cas.cz>
> Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed
> 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 Kol??
> Academy of Sciences of the Czech Republic
> Institute of Molecular Genetics
> V?de?sk? 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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