[Bioc-devel] lumi annotations

[Gang Feng]

Hi, Antti

example.lumi is an object of lumi.batch. For annotation, you can use lumiHumanAll.db
to get the mapping.

Best

Gilbert



> 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/
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
-----------------------------------------------------------------
Gang (Gilbert) Feng, PhD
Biomedical Informatics Center
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
750 N. Lake Shore Drive, 11th Floor(11-175e)
Chicago, IL  60611
Phone:312-503-2358
Email g-feng at northwestern.edu