Hi Bioconductors,

 

I am using R 2.4.1 and limma to analyze the new Agilent 4x44 array design
and am having trouble with the duplicate correlation function using the
following script:

 

library(limma)

targets <- readTargets("Targets.txt")

RG <- read.maimages(targets$FileName, source="agilent")

RG$genes<-readGAL()

RG$printer<-getLayout(RG$genes)

RG <- backgroundCorrect(RG, method="normexp", offset=50)

MA <- normalizeWithinArrays(RG, method="loess")

MA <- MA[order(RG$genes[,"ID"]),]

 

I get the following error:

 

Error in `[.MAList`(MA, order(RG$genes[, "ID"]), ) : 

        subscript out of bounds

 

I would like to treat the duplicate probes on each array as a technical
replicate, but since the spacing is not consistent for each gene, I must
first order the list by reference number. Are there any suggestions about
how I may do this?

 

Mitch

 

 

 

 

****************************************************************

Mitch Levesque, Ph.D.

Max Planck Institute for Developmental Biology

Department of Genetics and Genomics

Spemannstrasse 35/III

D-72076 Tübingen, GERMANY

 

Tel: +49 (0) 7071-601-401

Fax: +49 (0) 7071-601-384

****************************************************************

 


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