[BioC] loading CEL files in affylmGUI

James Wettenhall wettenhall at wehi.edu.au
Wed Jun 23 05:21:51 CEST 2004


I don't know much about the differences in the way the affy 
package handles different CEL file formats (binary or other),
but I can at least mention that affylmGUI expects you to set 
your working directory to the directory containing the CEL 
files, and then the CEL files listed in the Targets file don't 
need to have any absolute file paths, just a file name (expected 
to be in the current working directory).  I haven't tested much 
with Targets files that have absolute file paths.

Of course if you want to help us to isolate the error, you could 
try reading the CEL file at the command-line, with :
rawAffyData <- ReadAffy(filenames="foo.CEL")

Then you can tell whether the error is more related to affylmGUI 
or to affy.

Hope this helps,

 On Tue, 22 Jun 2004, Isaac Mehl wrote:

> i am having trouble opening my .CEL files in affylmGUI.  i get an error
> message:
> Failed to open file: "Foo.CEL"
> my best guess is that my .CEL files are all moe430a_2 and this does not
> have an annotation package.  or does this file need to be binary??
> afflmGUI 1.1.0
> limma 1.6.6
> R 1.9.0
> BioC 1.4
> -isaac
> --
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James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
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