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