[BioC] Can't load annotations with lumi

[Pan Du]

Hi Steve,

Since lumi 1.8, we have two types of libraries. One is for ID mapping
(mapping between Illumin IDs, nuIDs and RefSeq ID), which is named like
lumiHumanIDMapping. Another is for annotation only, which is named like
lumiHumanAll.db.

So your command should be like:
  x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng")

Also please update your lumi to version 1.8.2 if it is not, and read  the
vignette "IlluminaAnnotation.pdf".


Pan


On 11/20/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 1
> Date: Wed, 19 Nov 2008 12:23:36 +0000
> From: Steve Taylor <stephen.taylor at imm.ox.ac.uk>
> Subject: [BioC] Can't load annotations with lumi
> To: Bioconductor <bioconductor at stat.math.ethz.ch>
> Message-ID: <49240548.6070608 at imm.ox.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
> 
> I am trying to analyse some Illumina data using lumi. I have installed
> 'lumiHumanAll.db' but when I try and read in the Illumina file it seems to
> load all the data except the annotation information...
> 
>> x.lumi<-lumiR(fileName)
> Warning message:
> In addNuId2lumi(x.lumi, lib = lib) :
>    Please provide the annotation file or lumi annotation library!
> 
> If I include the name of the library...
> 
>> x.lumi<-lumiR(fileName,lib="lumiHumanAll.db")
> Warning messages:
> 1: In addNuId2lumi(x.lumi, lib = lib) :
>    lumiHumanAll.db does not include nuID conversion information!
> 2: In addNuId2lumi(x.lumi, lib = lib) :
>    Please provide the annotation file or lumi annotation library!
> 
>>  x.lumi
> Summary of BeadStudio output:
>          Illumina Inc. BeadStudio version 3.3.7
>          Normalization = none
>          Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml
>          Error Model = none
>          DateTime = 18/11/2008 18:43
>          Local Settings = en-GB
> 
> Major Operation History:
>              submitted            finished
> 1 2008-11-19 11:57:45 2008-11-19 11:57:57
> 2 2008-11-19 11:57:57 2008-11-19 11:58:00
>                                              command lumiVersion
> 1           lumiR("Sample_Probe_Profile.txt")       1.6.3
> 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh)       1.6.3
> 
> Object Information:
> LumiBatch (storageMode: lockedEnvironment)
> assayData: 48803 features, 24 samples
>    element names: beadNum, detection, exprs, se.exprs
> phenoData
>    sampleNames: AT1, AT2, ..., N12  (24 total)
>    varLabels and varMetadata description:
>      sampleID: The unique Illumina microarray Id
> featureData
>    featureNames: 6450255, 2570615, ..., 4120753  (48803 total)
>    fvarLabels and fvarMetadata description:
>      ProbeID: The Illumina microarray identifier
>      TargetID: The Illumina TargetID
> experimentData: use 'experimentData(object)'
> Annotation:
> Control Data: Available
> QC information: Please run summary(x, 'QC') for details!
> 
> I am using R version 2.7.1 (2008-06-23).
> 
>> packageDescription("lumi")
> Package: lumi
> Type: Package
> Title: BeadArray Specific Methods for Illumina Microarrays
> Version: 1.6.3
> Date: 2008-09-17
> Depends: R (>= 2.4.0), affy, mgcv (>= 1.4-0), methods
> Suggests: Biobase (>= 1.12.0), annotate, beadarray, limma, vsn,
>          lumiBarnes, lumiHumanAll.db, genefilter, geneplotter,
>          RColorBrewer
> Author: Pan Du, Warren Kibbe, Simon Lin
> Maintainer: Pan Du <dupan at northwestern.edu>
> Description: The lumi package provides an integrated solution for the
>          Illumina microarray data analysis. It includes functions of
>          Illumina BeadStudio data input, quality control,
>          BeadArray-specific variance stabilization, normalization and
>          gene annotation at the probe level.
> License: LGPL version 2 or newer
> biocViews: Microarray, OneChannel, Preprocessing
> Packaged: Thu Sep 18 02:54:06 2008; biocbuild
> Built: R 2.7.1; ; 2008-11-19 11:38:36; unix
> 
> My other question is (other than deleting the columns in the source files) if
> I QC an array and want to exclude it, how do I do that using the LumiBatch
> object?
> 
> The data is exported from BeadStudio version 3.3.7.
> 
> Thanks for any help,
> 
> Steve
> ------------------------------------------------------------------
> Medical Sciences Division
> Weatherall Institute of Molecular Medicine/Sir William Dunn School
> Oxford University