[BioC] simpleaffy error

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


Crispin,

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

David,

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.

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

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

Sorry about my earlier suggestion - I've now read the email
properly...
;-) 
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
and
get back to you..
Crispin
p.s. note that I've not tested things recently on windows:
http://bioinformatics.picr.man.ac.uk/simpleaffy 

-----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

* SNIP *
 
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