Dear All, I was trying to do a QC report for oligo generated mouse st gene array data, but was met with the errors: > library(affyQCReport) > library(affydata) > geneCore <- rma (affyGeneFS, target="core") Background correcting Normalizing Calculating Expression > featureData(geneCore) <- getNetAffx(geneCore, "transcript") > QCReport(geneCore, file="YuMGSt6QC.pdf") Error in box(...) : invalid 'which' argument In addition: Warning messages: 1: In plot.window(...) : "which" is not a graphical parameter 2: In plot.xy(xy, type, ...) : "which" is not a graphical parameter 3: In axis(side = side, at = at, labels = labels, ...) : "which" is not a graphical parameter 4: In axis(side = side, at = at, labels = labels, ...) : "which" is not a graphical parameter And, this happened after a recent updating of the R and BioC: > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0 oligoClasses_1.12.2 RColorBrewer_1.0-2 geneplotter_1.28.0 [6] annotate_1.28.0 annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 RSQLite_0.9-3 [11] DBI_0.2-5 AnnotationDbi_1.12.0 affyQCReport_1.28.1 lattice_0.19-13 simpleaffy_2.26.1 [16] genefilter_1.32.0 limma_3.6.9 affyPLM_1.26.0 preprocessCore_1.12.0 gcrma_2.22.0 [21] affydata_1.11.10 affy_1.28.0 Biobase_2.10.0 R.utils_1.5.7 R.oo_1.7.4 [26] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affxparser_1.22.1 affyio_1.18.0 Biostrings_2.18.2 grid_2.12.2 IRanges_1.8.9 splines_2.12.2 survival_2.36-1 tools_2.12.2 [9] xtable_1.5-6 I would appreciate any help I can get from the community. Best, Yongde

affyQCReport was designed to work with objects generated by 'affy', not by 'oligo', AFAIK. Try using 'affy' instead with the following annotation package: http://www.bioconductor.org/help/bioc- views/release/data/annotation/html/mogene10stv1cdf.html I hope to be able to add QC tools to oligo soon, but, in the meantime, consider the option above. b On 7 March 2011 14:57, YBao <yb8d at="" virginia.edu=""> wrote: > Dear All, > > I was trying to do a QC report for oligo generated mouse st gene array > data, but was met with the errors: > >> library(affyQCReport) >> library(affydata) >> geneCore <- rma (affyGeneFS, target="core") > Background correcting > Normalizing > Calculating Expression >> featureData(geneCore) <- getNetAffx(geneCore, "transcript") >> QCReport(geneCore, file="YuMGSt6QC.pdf") > Error in box(...) : invalid 'which' argument > In addition: Warning messages: > 1: In plot.window(...) : "which" is not a graphical parameter > 2: In plot.xy(xy, type, ...) : "which" is not a graphical parameter > 3: In axis(side = side, at = at, labels = labels, ...) : > ?"which" is not a graphical parameter > 4: In axis(side = side, at = at, labels = labels, ...) : > ?"which" is not a graphical parameter > > And, this happened after a recent updating of the R and BioC: > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0 > oligoClasses_1.12.2 ? ? ? RColorBrewer_1.0-2 ? ? ? ?geneplotter_1.28.0 > ?[6] annotate_1.28.0 ? ? ? ? ? annaffy_1.22.0 ? ? ? ? ? ?KEGG.db_2.4.5 > ? ? ? ? ? ?GO.db_2.4.5 ? ? ? ? ? ? ? RSQLite_0.9-3 > [11] DBI_0.2-5 ? ? ? ? ? ? ? ? AnnotationDbi_1.12.0 > affyQCReport_1.28.1 ? ? ? lattice_0.19-13 ? ? ? ? ? simpleaffy_2.26.1 > [16] genefilter_1.32.0 ? ? ? ? limma_3.6.9 > affyPLM_1.26.0 ? ? ? ? ? ?preprocessCore_1.12.0 ? ? gcrma_2.22.0 > [21] affydata_1.11.10 ? ? ? ? ?affy_1.28.0 > Biobase_2.10.0 ? ? ? ? ? ?R.utils_1.5.7 ? ? ? ? ? ? R.oo_1.7.4 > [26] R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.22.1 affyio_1.18.0 ? ? Biostrings_2.18.2 grid_2.12.2 > ? ? IRanges_1.8.9 ? ? splines_2.12.2 ? ?survival_2.36-1 > tools_2.12.2 > [9] xtable_1.5-6 > > I would appreciate any help I can get from the community. > > Best, > > Yongde > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >