[BioC] affy package problem

[Ben Bolstad]

This bug is now fixed (as of affy 1.4.3). You'll have to wait for the
overnight builds to go through to use it. As noted, don't use affy 1.4.2
for reading text cel files on windows, it does seem to like to delete
cel files.

Ben


On Tue, 2003-12-02 at 06:09, James MacDonald wrote:
> Correction: There is a bug in the Win32 version of affy 1.4.2. The *nix
> version appears to work fine for text .cel files.
> 
> 
> 
> 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
> 
> >>> "James MacDonald" <jmacdon at med.umich.edu> 12/02/03 09:01AM >>>
> It appears that there is a bug in 1.4.2 that causes it to not read
> text
> .cel files. For now, I would recommend reverting to the release
> version
> for non-binary .cel files.
> 
> 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
> 
> >>> <Phguardiol at aol.com> 12/02/03 04:51AM >>>
> Hi all,
> I m trying to use Affy 1.4.2 with U133A chips on a new PC P4 with XP
> Pro and R 1.8.1
> I m selecting the right Folder first where my CEL files are and then
> paste on the command line: 
> data1 <- ReadAffy()
> data2 <- gcrma(data1)
> exprs2excel(data2, file="Fibroalone_gcrma.csv")
> 
> then I obtain the following:
> > library(affy)
> Welcome to Bioconductor 
>          Vignettes contain introductory material.  To view, 
>          simply type: openVignette() 
>          For details on reading vignettes, see
>          the openVignette help page.
> 
> Synching your local package management information ...
> Packages which have been added/updated:
>         matchprobes
>         arrayMagic
>         externalVector
>         limma
>         
> 
> > library(gcrma)
> Loading required package: MASS 
> > data1 <- ReadAffy()
> Error in initialize(value, ...) : Could not open file C:/Phil/CEL
> files
> Fibro alone/FANC Fibro/fibro PD331neo01.CEL
> > data2 <- gcrma(data1)
> Error: Object "data1" not found
> Error in probeNames(object) : Unable to find the argument "object" in
> selecting a method for function "probeNames"
> > exprs2excel(data2, file="Fibroalone_gcrma.csv
> 
> and in addition, the CEL file is no more present in the folder as if
> it
> was deleted...!
> Any suggestion ?
> Thanks
> Philippe
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad