[BioC] affy package problem

[James MacDonald]

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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