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