Question: Normalization of Illumina Array with separate bgx-file
0
5.8 years ago by
Stefanie Busch10 wrote:
annotation limma beadarray bgx • 1.7k views
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
0
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}}