[BioC] About Illumina annotation packages lumixxxAll.db

[Pan Du]

Hi Bob,

The lumiMouseAll.db (or lumiHumanAll.db and lumiRatAll.db) only includes the
annotation information of the probe. It does not include the Illumina ID and
nuID mapping information. The reason is that the recent versions of
BeadStudio always output the probe sequence information together with the
data. So the lumiR can automatically convert  the probe sequences as nuIDs
without needing any libraries.

For your case, because your data is in old version (v1.1), it may not
include the probe sequence in the file. So you need to map the Illumina ID
to nuID first by using package lumiMouseV1 like this:

 x.lumi <- lumiR(fileName,lib='lumiMouseV1')

Later on, if you want to retrieve the annotation information, you can
directly use lumiMouseAll.db, which is in the same format as other
Bioconductor annotation .db packages.

We are also trying to set up an online service to mapping different Illumina
IDs to nuIDs and then retrieve annotation information.
Tell me if you have other questions.


Pan


On 5/2/08 12:35 PM, "Robert Searles" <searlesr at ohsu.edu> wrote:

> Pan,
> 
> I'm using R 2.70 and BioConductor 2.2.
> 
> I previously had used lumiMouseV1 as the annotations file, but for this
> set-up, I used the new lumiMouseAll.db library.  The data file is for a
> set of MouseWG6 v1.1 arrays.
> 
> I run the lumi protocol as follows:
> 
>> library(lumi)
>> library(lumiMouseAll.db)
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
>> fileName <- "c:/RH248_1_Group_Probe_Profile.txt"
>> x.lumi <- lumiR(fileName,lib='lumiMouseAll.db')
> Warning messages:
> 1: In addNuId2lumi(x.lumi, lib = lib) :
>   lumiMouseAll.db does not include nuID conversion information!
> 2: In addNuId2lumi(x.lumi, lib = lib) :
>   Please provide the annotation file or lumi annotation library!
> 
> I get the two warning messages, which indicate that there is another
> file needed to get the nuID conversions.  Is that correct or am I doing
> something wrong?
> 
> Bob
> 
> 
> 
>>>> "Pan Du" <dupan at northwestern.edu> 5/1/2008 9:12:04 AM >>>
> Hi Bob,
> 
> Yes. It is the lumiMouseAll.db package. The package is in the
> Bioconductor
> developing version (Bioc 2.2), which will be released very soon. You
> need to
> use R2.7 if you use biocLite to install it. You can also manually
> download
> and install it if you are using early R versions. Tell me if you meet
> any
> problems when using it. We are also setting up a website for Illumina
> ID
> mapping.
> 
> 
> Pan
> 
> 
> On 5/1/08 11:03 AM, "Robert Searles" <searlesr at ohsu.edu> wrote:
> 

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