[BioC] simpleaffy error

James MacDonald jmacdon at med.umich.edu
Fri Jul 2 15:40:36 CEST 2004


I don't think it has to do with using '/' as a path separator on
Windows, because this works for me.


Is your covdesc by chance called covdesc.txt? If I have a file named
covdesc in my working directory, it works fine. If the file is missing
or has a .txt subscript, then I get the error you report.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Crispin Miller" <CMiller at PICR.man.ac.uk> 07/02/04 07:50AM >>>

Sorry about my earlier suggestion - I've now read the email
I suspect that it's a problem with using '/' as a path separator on
Windows... (I see you're using a Windows system...) I'll have a play
get back to you..
p.s. note that I've not tested things recently on windows:

-----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
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
number of samples=6 number of genes=22283 annotation=hgu133a

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