[Bioc-devel] lumi annotations

[Pan Du]

Hi Antti 

"lumiHumanV1.db" is the old annotation package for Illumina Human V1 chip,
which was used when creating the example.lumi dataset. It is not supported
now. The current nuID indexed Illumina annotation package for Human is
"lumiHumanAll.db", which pools all versions of Illumina Human Beadchip.
It works fine if you use "lumiHumanAll.db" annotation package.
 biocLite("lumiHumanAll.db")
 m <- getAnnMap('SYMBOL', "lumiHumanAll.db")
 get(featureNames(example.lumi)[1], m)

Also, I will update the annotation information of example.lumi dataset
later.


Pan

On 12/17/10 5:00 AM, "bioc-devel-request at r-project.org"
<bioc-devel-request at r-project.org> wrote:

> Date: Fri, 17 Dec 2010 11:06:55 +0200
> From: Antti Honkela <antti.honkela at tkk.fi>
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] lumi annotations
> Message-ID: <A8C5841E-4FCF-43CE-9FB0-EA3DB2E17A8C at tkk.fi>
> Content-Type: text/plain; charset=WINDOWS-1252; format=flowed;
> delsp=yes
> 
> Hi all,
> 
> I am developing a package with intention to use data from several
> microarray platforms and the related annotations in a portable manner.
> 
> Given an ExpressionSet "eset", I have been using constructs like
>> library(annotate)
>> m <- getAnnMap('SYMBOL', annotation(eset))
>> s <- get(featureNames(eset)[1], m)
> which seems portable and works fine on Affymetrix data I have used so
> far.
> 
> Turning to Illumina and lumi package the same does not work anymore:
> ------------------------------------------------------------
>> library(lumi)
>> data(example.lumi)
>> m <- getAnnMap('SYMBOL', annotation(example.lumi))
> Error: getAnnMap: package lumiHumanV1 not available
>> biocLite('lumiHumanV1.db')
> Using R version 2.12.0, biocinstall version 2.7.4.
> Installing Bioconductor version 2.7 packages:
> [1] "lumiHumanV1.db"
> Please wait...
> 
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ?lumiHumanV1.db? is not available
> ------------------------------------------------------------
> 
> Is this just a bug in the example.lumi object, or is it simply wrong
> to assume that the same mechanism should work with lumi at all?
> 
> 
> Antti
> 
> -- 
> Antti Honkela
> Antti.Honkela at tkk.fi   -   http://users.ics.tkk.fi/ahonkela/
> 
> 


--
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