[BioC] Can't load annotations with lumi

Steve Taylor stephen.taylor at imm.ox.ac.uk
Wed Nov 19 13:23:36 CET 2008


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
   sampleNames: AT1, AT2, ..., N12  (24 total)
   varLabels and varMetadata description:
     sampleID: The unique Illumina microarray Id
   featureNames: 6450255, 2570615, ..., 4120753  (48803 total)
   fvarLabels and fvarMetadata description:
     ProbeID: The Illumina microarray identifier
     TargetID: The Illumina TargetID
experimentData: use 'experimentData(object)'
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,
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,

Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University

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