[BioC] One-Color Aglent Data into Limma GUI

[Ido M. Tamir]

On Tuesday 09 October 2007 06:32, elliot harrison wrote:
> Hi All,
>
> I'm trying to work with One-color agilent data without much luck.
> http://article.gmane.org/gmane.science.biology.informatics.conductor/128
> 18/match=agilent
>
> I've tried the above method but as I posted before I get stuck on the
> following error.
>
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
> Specified column headings not found in file

samples <- readTargets("SampleKey.txt",sep="\t")[resort,]
raw<-read.maimages(files=samples$fileName,path="RawData",columns=list(R="IsUsedBGAdjust",G="gProcessedSignal"))
genes<-read.table(paste("RawData/",samples$fileName[1],sep=""),sep="\t",as.is=TRUE,skip=9,header=TRUE,quote="",fill=TRUE)
genes <- genes[,1:15]
expressionValues <- raw$G
rownames(expressionValues) <- genes$FeatureName
colnames(expressionValues) <- samples$description

the IsUsedBGAdjust is a column full of 0s

and from this I then decided to construct an expressionset,
which I found out is quite verbose and tedious and I don't yet 
see a lot of gain there.

I also see a probe GC content bias in the intensity levels and have not
yet decided if and how to deal with it. 

best wishes
ido