Question: Normalization of Illumina Array with separate bgx-file
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gravatar for Stefanie Busch
5.8 years ago by
Stefanie Busch10 wrote:
Hello, I'm Stefanie from Germany. So excuse me when my english isn't very well. I want to normalize the raw data of the GEO experiment "GSE39313". In this experiment the Illumina MouseRef-8 v2.0 expression beadchip was used. I get the data with getGEOSuppFiles but I don't know what I should do next. I know that I can analyse Illumina chips with the packages beadarray, lumi or limma. I have uploaded the raw.txt-file with the different packages. For example: > Daten.lumi<-lumiR(file="GSE39313_non-normalized.txt") Please provide Illumina ID Mapping library! > Daten.lumi ExpressionSet (storageMode: lockedEnvironment) assayData: 25697 features, 48 samples element names: detection, exprs protocolData: none phenoData sampleNames: 7539447003_A 7539447003_B ... 7917911031_H (48 total) varLabels: sampleID varMetadata: labelDescription featureData featureNames: ILMN_2896528 ILMN_2721178 ... ILMN_2424408 (25697 total) fvarLabels: ID_REF fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: As you can see I have no Annotation information. GEO provide the bgx.file for the Chip (Illumina MouseRef-8 v2.0 expression beadchip) but I don't know how to connect this. I tried this: > Daten.lumi2<-addNuID2lumi(Daten.lumi,annotationFile="MouseRef- 8_V2_0_R3_1127 8551_A.bgx") > Daten.lumi2 ExpressionSet (storageMode: lockedEnvironment) assayData: 25697 features, 48 samples element names: detection, exprs protocolData: none phenoData sampleNames: 7539447003_A 7539447003_B ... 7917911031_H (48 total) varLabels: sampleID varMetadata: labelDescription featureData featureNames: WpaZ9x9f_hAnoR.VBE ZhdXp75JftSF3iWLF4 ... Zl4J4B0PsjTJ1N19IM (25697 total) fvarLabels: ID_REF fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: But there are again no annotation Information. And when I used the exprs() function I get this what looks very strange: > head(exprs(Daten.lumi2)) 7539447003_A 7539447003_B 7539447003_C 7539447003_D WpaZ9x9f_hAnoR.VBE 4476.8840 5870.2020 5149.9380 5193.5800 ZhdXp75JftSF3iWLF4 970.4051 1032.8760 1132.4740 1280.3510 xnx7ijE2CcOSlY55eA 1577.7980 1511.4770 1711.2830 1850.6020 xPkUXaq37oR_vSi6HY 9862.2040 11187.4000 12783.4400 14389.9900 3rtRBd9AcK1Qq07fGI 222.3842 236.7587 210.8107 229.3236 ZqRKnn0K14kTIep1.c 3877.7640 5116.4140 6129.5220 2486.4500 So I tried to use limma: > Daten.limma<-read.ilmn(files="GSE39313_non- normalized.txt",other.columns="De tection Pval") This works well, but I don't know where to get the bgx.file in. And the further problem is, when I want to normalize according to the instructions of BeadArrayUseCases page 25 I get this error message: > maqc.norm<-neqc(Daten.limma) Fehler in normexp.fit.detection.p(x, detection.p) : Detection p values not found in the data. Please can you tell me where is my mistake? Stefanie
annotation limma beadarray bgx • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Gordon Smyth39k • written 5.8 years ago by Stefanie Busch10
Answer: Normalization of Illumina Array with separate bgx-file
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gravatar for Gordon Smyth
5.8 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:
Dear Stefanie, > Date: Fri, 7 Feb 2014 14:27:58 +0100 > From: "Stefanie Busch" <tiffi_88 at="" web.de=""> > To: bioconductor at r-project.org > Subject: [BioC] Normalization of Illumina Array with separate bgx- file > > Hello, > > I'm Stefanie from Germany. So excuse me when my english isn't very well. > > I want to normalize the raw data of the GEO experiment "GSE39313". In > this experiment the Illumina MouseRef-8 v2.0 expression beadchip was > used. I get the data with getGEOSuppFiles but I don't know what I should > do next. I know that I can analyse Illumina chips with the packages > beadarray, lumi or limma. I have uploaded the raw.txt-file with the > different packages. ... > So I tried to use limma: > > Daten.limma<-read.ilmn(files="GSE39313_non- normalized.txt",other.columns="De > tection Pval") > > This works well, but I don't know where to get the bgx.file in. It would be simpler to read the text annotation file from GEO. Go to the URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6885 Click on "Download full table" and save the file to disk. Then ann <- read.delim("GPL6885-11608.txt",comment.char="#",quote="") m <- match(rownames(Daten.limma), ann$ID) Daten.limma$genes <- ann[m,] > And the further problem is, when I want to normalize according to the > instructions of BeadArrayUseCases page 25 I get this error message: > > > maqc.norm<-neqc(Daten.limma) > Fehler in normexp.fit.detection.p(x, detection.p) : > Detection p values not found in the data. You need neqc(Daten.limma,detection.p="Detection Pval") Best wishes Gordon > Please can you tell me where is my mistake? > > > Stefanie ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 5.8 years ago by Gordon Smyth39k
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