Dear R helpers, I'm an R beginner who is learning 'arrayQualityMetrics' package. The package is very handy and clear. It greatly improves both my knowledge and analytic results. I'm reading 'Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output'. After reading outliners' observation in aqm.boxplot object, I'm wondering whether I can observe Hoeffding's statistic Da in aqm.maplot object? Would you please show me how to do it? Best Regards, Kaj Chokeshaiusaha -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.16.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 affyPLM_1.36.0 [4] annotate_1.38.0 AnnotationDbi_1.22.6 beadarray_2.10.0 [7] BeadDataPackR_1.12.0 Biobase_2.20.1 BiocGenerics_0.6.0 [10] BiocInstaller_1.10.3 Biostrings_2.28.0 Cairo_1.5-2 [13] cluster_1.14.4 colorspace_1.2-3 DBI_0.2-7 [16] gcrma_2.32.0 genefilter_1.42.0 grid_3.0.1 [19] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.3 [22] lattice_0.20-23 latticeExtra_0.6-24 limma_3.16.8 [25] parallel_3.0.1 plyr_1.8 preprocessCore_1.22.0 [28] RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-3 [31] RSQLite_0.11.4 setRNG_2011.11-2 splines_3.0.1 [34] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 [37] SVGAnnotation_0.93-1 vsn_3.28.0 XML_3.98-1.1 [40] xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Kaj Yes. If 'x' is the result of a call to aqm.maplot , then x at out is an object of class "outlierDetection", and x at out@stat is Hoeffding's statistic. Best wishes wolfgang On 23 Sep 2013, at 05:46, Kaj Chokeshaiusaha [guest] <guest at="" bioconductor.org=""> wrote: > > Dear R helpers, > > I'm an R beginner who is learning 'arrayQualityMetrics' package. The package is very handy and clear. It greatly improves both my knowledge and analytic results. > > I'm reading 'Advanced topics: Customizing arrayQualityMetrics reports and > programmatic processing of the output'. After reading outliners' observation in aqm.boxplot object, I'm wondering whether I can observe Hoeffding's statistic Da in aqm.maplot object? > > Would you please show me how to do it? > > Best Regards, > Kaj Chokeshaiusaha > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.16.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 affyPLM_1.36.0 > [4] annotate_1.38.0 AnnotationDbi_1.22.6 beadarray_2.10.0 > [7] BeadDataPackR_1.12.0 Biobase_2.20.1 BiocGenerics_0.6.0 > [10] BiocInstaller_1.10.3 Biostrings_2.28.0 Cairo_1.5-2 > [13] cluster_1.14.4 colorspace_1.2-3 DBI_0.2-7 > [16] gcrma_2.32.0 genefilter_1.42.0 grid_3.0.1 > [19] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.3 > [22] lattice_0.20-23 latticeExtra_0.6-24 limma_3.16.8 > [25] parallel_3.0.1 plyr_1.8 preprocessCore_1.22.0 > [28] RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-3 > [31] RSQLite_0.11.4 setRNG_2011.11-2 splines_3.0.1 > [34] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 > [37] SVGAnnotation_0.93-1 vsn_3.28.0 XML_3.98-1.1 > [40] xtable_1.7-1 zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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