[BioC] identical output plots for NUSE AND RLE

[Richard Friedman]

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