[BioC] affy package problem

James MacDonald jmacdon at med.umich.edu
Tue Dec 2 15:01:08 MET 2003

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.


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> <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:

> 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 ?

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