[BioC] arrayQualityMetrics: How to observe Hoeffding\'s statistic Da in aqm.maplot object?

[Wolfgang Huber]

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.
> 
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