[R] Question regarding reading arrayvision files in limma

From: Debayan Datta <debayan.datta_at_yale.edu>
Date: Fri 26 May 2006 - 04:31:38 EST


Hi Everyone,

     I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some
problem. My code is :

setwd('C:/work/data/limma/ndd1');
files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t");

#Normalisation
MA=normalizeWithinArrays(RG);
#plotPrintTipLoess(MA);
#Fit Linear model and Empirical Bayes method fit=lmFit(MA);
fit <- eBayes(fit) ;
res=topTable(fit,sort.by="P",number=7200); hist(res$P.Value,breaks=50);

The error message I get is :

Read ndd1_1.txt
Read ndd1_2.txt
Read ndd1_3.txt

Error in switch(method, loess = { : Layout argument not specified

I then created a layout file and added in the following code, but I still got the same error message.

RG$genes=readGAL();
gal=readGAL();
layout=getLayout(gal);

Also, when I type RG , I get,

> RG
An object of class "RGList"
$R

[1] 3

$Rb

[1] 6

$G

[1] 10

$Gb

[1] 14

$targets

          FileName

ndd1_1 ndd1_1.txt
ndd1_2 ndd1_2.txt
ndd1_3 ndd1_3.txt

$source

[1] "arrayvision"

$genes

   Block Row Column    ID           Name
1     1   1      1 my_ID my_Description
2     1   1      2 my_ID my_Description
3     1   1      3 my_ID my_Description
4     1   1      4 my_ID my_Description
5     1   1      5 my_ID my_Description

7195 more rows ...

Thus, its not reading the data in the 2 forground and background channels, just the column indices.

Could you please suggest what I am doing wrong? Thank you for your time!

Debayan



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