[BioC] AffyExpress: AffyQA incompatible with simpleaffy 2.14.04?

[Stefan Thomsen]

Dear all,

previously, AffyQA in AffyExpress could not return certain plots on my data 
as my Drosophila Genome 2.0 chips were not defined in simpleaffy. The newly 
released simpleaffy version 2.14.04 allows now easy manual chip definition.

However, if I run now AffyQA() after calling library(simpleaffy) and 
defining my chips's QC-envirionment using setQCEnvironment(), I get the 
following error message:


> AffyQA(parameters=c("time", "treatment"), raw=affybatch.raw)

Error in setQCEnvironment(name) : 
  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. In 
addition: Warning message: This function is DEPRECATED and WILL disappear 
from future versions of simpleaffy. Please see 
help("simpleaffy-deprecated") for more details.
 


This error method comes from within the new simpleaffy qc() function, 
hence, could it be that AffyExpress incompatible with the current 
simpleaffy package?

If yes, what would be an elegant way to circumvent this? 


Kind regards,

Stefan







> 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_2.14.04 genefilter_1.16.0 survival_2.32 affyPLM_1.14.0 
gcrma_2.10.0
 [6] matchprobes_1.10.0 R2HTML_1.58 AffyExpress_1.2.0 limma_2.12.0 
affy_1.16.0 [11] 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