[BioC] simpleaffy error

[kfbargad at lg.ehu.es]

Dear James,

I have tried typing the following:

> raw.data<-read.affy("covdesc.txt")
Error in read.affybatch(filenames = filenames, phenoData = 
phenoData,  : 
        Could not open file ./DEP014HA

But I can still read in my Cel files with affy:

> raw.data <- ReadAffy()
> raw.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

David




> 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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> 
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