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Steve Taylor
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@steve-taylor-2838
Last seen 10.3 years ago
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
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University