[BioC] identical output plots for NUSE AND RLE

[Richard Friedman]

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
>>
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>>
>
> -- 
> Paolo Innocenti
> Department of Animal Ecology, EBC
> Uppsala University
> Norbyvägen 18D
> 75236 Uppsala, Sweden
>
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