[BioC] identical output plots for NUSE AND RLE

[Ben Bolstad]

You might want to try using the NUSE() and RLE() functions directly rather 
than the boxplot method.

Best,

Ben

--------------------------------------------------
From: "Richard Friedman" <friedman at cancercenter.columbia.edu>
Sent: Tuesday, June 22, 2010 6:32 AM
To: "bio c bioconductor" <bioconductor at stat.math.ethz.ch>
Subject: [BioC] identical output plots for NUSE AND RLE

> Dear List,
>
> I got identical plots for RLE and NUSE using affyPLM.
> My script up to the point that the plots were generated is:
>
> #battery of quality tests
> library(affy)
> library(affyPLM)
> library(affyQCReport)
> library(simpleaffy)
> library(gcrma)
> library(limma)
> library(arrayQualityMetrics)
> library(genefilter)
> library(rgl)
> library(affycoretools)
> library(scatterplot3d)
>
> raw<-ReadAffy()
> plm<-fitPLM(raw)
> png("NUSE.png")
> boxplot(plm,main="NUSE")
> dev.off()
> png("RLE.png")
> boxplot(plm,main="RLE")
> dev.off()
>
> My sessionInfo is:
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-apple-darwin9.8.0
>
> 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] mouse4302probe_2.6.0      mouse4302cdf_2.6.0 
> scatterplot3d_0.3-30
>  [4] affycoretools_1.20.0      KEGG.db_2.4.1             GO.db_2.4.1
>  [7] RSQLite_0.9-0             DBI_0.2-5 
> AnnotationDbi_1.10.1
> [10] rgl_0.91                  arrayQualityMetrics_2.6.0 limma_3.4.0
> [13] affyQCReport_1.26.0       lattice_0.18-5 
> RColorBrewer_1.0-2
> [16] xtable_1.5-6              simpleaffy_2.24.0 
> genefilter_1.30.0
> [19] affyPLM_1.24.0            preprocessCore_1.10.0     gcrma_2.20.0
> [22] affy_1.26.1               Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.16.0       annaffy_1.20.0      annotate_1.26.0 
> beadarray_1.16.0    biomaRt_2.4.0
>  [6] Biostrings_2.16.0   Category_2.14.0     GOstats_2.14.0 
> graph_1.26.0        grid_2.11.0
> [11] GSEABase_1.10.0     hwriter_1.2         IRanges_1.6.1 
> latticeExtra_0.6-11 marray_1.26.0
> [16] RBGL_1.24.0         RCurl_1.4-2         splines_2.11.0 
> stats4_2.11.0       survival_2.35-8
> [21] tools_2.11.0        vsn_3.16.0          XML_3.1-0
> >
>
> In the past my NUSE and RLE plots looked different, as I wold expect  on 
> theoretical grounds.
> If anyone is willing to look at  the plots i am happy to do send them  off 
> list,
>
> Thanks and best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In Memoriam,
> George Scithers
>
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