[BioC] simpleaffy error

[Crispin Miller]

Hi,
Do you have a file in the directory called 'covdesc'... It should
contain the information about your experimental factors for your arrays:

For example:

		A	B
One.cel	n	n	
Two.cel	n	y	
Three.cell	y	y
Four.cel	n	n
Five.cel	n	y
Six.cel	y	y
Seven.cel	n	n
Eight.cel	n	y
Nine.cel 	y	y

These end up in the pData slot of the AffyBatch object that gets read
in...

(you can specify the name of the file you are looking for: eset <-
covdesc("my.design.file") or whatever)...
Crispin



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
kfbargad at lg.ehu.es
Sent: 02 July 2004 07:50
To: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] simpleaffy error

Thanks Jim for your quick answer. My working directory is the right one
because if I use the affy package I can read in the data:

> library(simpleaffy)
> library(affy)
> raw.data <- read.affy()
Error in file(file, "r") : unable to open connection In addition:
Warning message: 
cannot open file `./covdesc' 
> Data <- ReadAffy()
> Data
AffyBatch object
size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids)
number of samples=6 number of genes=22283 annotation=hgu133a


> That error usually indicates that you have not set the working
directory
> to the directory containing your files.
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> <kfbargad at lg.ehu.es> 07/01/04 12:58PM >>>
> 
> Dear users,
> 
> I have created a directory with a white-space delimited file 
> describing my samples called "covdesc" as suggested and have all the 
> CEL files in the same directory
> 
> I have loaded simpleaffy library and tried to read in the data. I
get 
> 
> an error that has been previously mentioned but couldn t find the 
> solution in the Bioconductor Archives. This is what I type and the 
> error
> 
> > raw.data <- read.affy()
> Error in file(file, "r") : unable to open connection In addition: 
> Warning message:
> cannot open file `./covdesc'
> 
> I am working on a Windows 2000 computer R version 1.9.1 BioC version 
> 1.4
> 
> any suggestions?
> 
> 
> Thanks in advance
> 
> David
> 
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