[BioC] How to convert Illumina ProbeIDs to nuIDs without nuID indexed annotation libraries?

[Pan Du]

Hi Elliot,

Sorry for replying late for your last email.
For some reason, we have not created the ID mapping package for Rat chip yet
and it will not included in the Bioc 2.3. We will create one in the future.
However, you can use lumiRatV1 for the id conversion because there is no new
Illumina Rat chip was released. You need to install both lumiRatV1 (you have
to manually download in from Bioc 2.1.) and lumiRatAll.db packages.
lumiRatV1 is just for ID mapping purpose and lumiRatAll.db is for latest
annotation. Thanks!


Pan



On 9/25/08 12:39 PM, "Elliot Kleiman" <kleiman at rohan.sdsu.edu> wrote:

> Hi Pan,
> 
> I was wondering, do you have a plan to release a nuID indexed
> annotation mapping for the Rat for BioC release 2.3?
> e.g., lumiRatIDMapping.db'
> 
> RE: I did not see an equivalent, 'lumiRatIDMapping.db' package on
> the devel site for BioC 2.3 or am I wrong?
> * http://www.bioconductor.org/packages/2.3/data/annotation/
> 
> Thank you,
> 
> ... Elliot
> 
> Pan Du wrote:
>> Hi Elliot,
>> 
>> You can find the Illumina ID mapping packages, lumiHumanIDMapping.db and
>> lumiMouseIDMapping.db, in the Bioc 2.3 (Developing). These packages include
>> all types of Illumina IDs and corresponding nuIDs. To do ID mapping, you
>> also need to update the lumi package to the developing version lumi 1.7.23.
>> Please read the vignette "IlluminaAnnotation.pdf" before using them. All
>> these packages can be installed and ran in R 2.7 or above. If you are using
>> R 2.7, you need to manually download and install them,  biocLite cannot
>> install developing version packages.
>> Tell me if you have any questions.
>> 
>> 
>> Pan
>> 
>> 
>> 
>> On 9/23/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
>> <bioconductor-request at stat.math.ethz.ch> wrote:



------------------------------------------------------
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan at northwestern.edu