Entering edit mode
Richard Friedman
★
2.0k
@richard-friedman-513
Last seen 10.2 years ago
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