[BioC] simpleaffy 2.14.02, setQCEnvironment

[Stefan Thomsen]

Dear all,

I am trying to perform some simpleaffy analyses on Drosophila Genome 2.0 
genechips. Following the instructions of the simpleaffy 2.14.02 vignette I 
set up the following .qcdef file:

array drosophila2cdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD AFFX-r2-Ec-bioD-3_at
spk creX AFFX-r2-P1-cre-3_at
ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at
ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_f_at
ratio gapdh3/gapdh5 AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_5_at
ratio gapdh3/gapdhM AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_M_at

I saved it as drosophila2cdf.qcdef.txt and removed the file extension .txt 
afterwards.

When I try to run qc() on my affybatch and affybatch.mas5 (created by 
calling call.exprs(affybatch, "mas5") objects I get the following error 
message:

> library(simpleaffy)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: gcrma
Loading required package: matchprobes

> setQCEnvironment("drosophila2cdf", "/Users/Stefan")   
> qc.data=qc(affybatch.raw, affybatch.mas5)
Error in setQCEnvironment(cdfn) : 
  Could not find array definition file ' drosophila2cdf.qcdef '. Simpleaffy 
does not know the QC parameters for this array type. See the package 
vignette for details about how to specify QC parameters manually.


I confess, my programming skills are rather limited. However, I tried to 
look at setQCEnvironment() and its subfunction qc.read.file(). If I 
directly assign the .qcdef file including its path to the 'fn' argument, 
qc.read.file seems to be able to open, read and print the lines of my file.

Thus, why do keep on running into this error?

Any help on this issue would be highly appreciated.


My sessionInfo is as follows:

> sessionInfo()
R version 2.6.0 (2007-10-03) 
powerpc-apple-darwin8.10.1 

locale:
en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages: [1] splines tools stats graphics grDevices utils 
datasets methods base

other attached packages: [1] simpleaffy_2.14.02 gcrma_2.10.0 
matchprobes_1.10.0 genefilter_1.16.0 survival_2.32 affy_1.16.0 [7] 
preprocessCore_1.0.0 affyio_1.6.0 Biobase_1.16.0

loaded via a namespace (and not attached): [1] AnnotationDbi_1.0.4 
DBI_0.2-3 RSQLite_0.6-3 annotate_1.16.0
> 
-- 
Dr. Stefan Thomsen
Research Associate

Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ

Tel.: +44 1223 336623 
Fax:  +44 1223 336679

stt26 at cam.ac.uk