[Bioc-devel] lumi annotations

Antti Honkela antti.honkela at tkk.fi
Fri Dec 17 10:06:55 CET 2010

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  

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 Honkela
Antti.Honkela at tkk.fi   -   http://users.ics.tkk.fi/ahonkela/

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