R help - May 2006 - Question regarding reading arrayvision files in limma

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

Dear Debayan,

I only use Genepix files but I will try to help you with the experience I
have concerning layout troubleshooting and limma.

First : RG$R, RG$Rb, RG$G and RG$Gb seem strange to me. As I understand
these data, it has to be a vector of the same length than the number of
spots.
It seems to me like if it was the layout of your chip, and as 3*6*10*14=2520
which is very different from 7195 that you have in RG$genes, maybe the
problem is here (that there is more spots that announced by the layout ?

Second : I had problems when there is blocks with incomplete line(s). It
seems to me (but I did not push so far so maybe Gordon Smyth will correct
me) that the function getLayout() assumes that the block on the chip are
entire, so if it is not the case it is waiting for more spots that it
effectively finds in the data.
Finally, what do you have in RG$ngrid.c, RG$ngrid.r etc .. ?

HTH

Florence.


On 5/25/06, Debayan Datta <debayan.datta@yale.edu>
wrote:
>
> 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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