[BioC] One-Color Aglent Data into Limma GUI

Ido M. Tamir tamir at imp.univie.ac.at
Tue Oct 9 12:50:43 CEST 2007

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,]
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

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