[Bioc-devel] lumi annotations

Martin Morgan mtmorgan at fhcrc.org
Fri Dec 17 14:16:18 CET 2010


On 12/17/2010 01:06 AM, Antti Honkela wrote:
> 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?

Hi Antti --

This is the right approach; both the annotation package and 'map' have
to exist; from

http://bioconductor.org/help/bioc-views/release/data/annotation/

I think the correct annotation package name is 'illuminaHumanv1.db'.
Most maps are common across chip / organism, but for instance there are
'ORF' maps in yeast-centric packages such as yeast2.db but not elsewhere.

Martin

> 
> 
> Antti
> 


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