Paolo, Thanks. It worked., I must have changed teh script through a pasting error. Best wishes, Rich On Jun 22, 2010, at 9:45 AM, Paolo Innocenti wrote: > Try with: > > # RLE > Mbox(plm, main="RLE") > # > # NUSE > boxplot(plm, main="NUSE") > > more info at section 3.5.1 (pag.45) of > "Bioinformatics and computational biology solutions using R and > BioConductor", Gentleman R. et al. (2004). > > best, > paolo > > > On 06/22/2010 03:32 PM, Richard Friedman wrote: >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Paolo Innocenti > Department of Animal Ecology, EBC > Uppsala University > Norbyv?gen 18D > 75236 Uppsala, Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor