[BioC] Normalization of Illumina Array with separate bgx-file

[Gordon K Smyth]

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

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