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/