Question: Problem with BGandNorm() from the Agi4x44PreProcess package
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gravatar for Dick Beyer
8.4 years ago by
Dick Beyer1.4k
Dick Beyer1.4k wrote:
Hello, I've run into a problem that looks like the function BGandNorm() is broken because it relies on vsn as a method called by normalizeBetweenArrays, but that method has been replaced by a function normalizeVSN(). Here is some output that shows the problem: > dd <- read.AgilentFE(targets, makePLOT=FALSE) Read US23502338_252643710125_S01_GE1_107_Sep09_1_4.txt Read US23502338_252643710125_S01_GE1_107_Sep09_1_3.txt Read US23502338_252643710125_S01_GE1_107_Sep09_1_2.txt Read US23502338_252643710125_S01_GE1_107_Sep09_1_1.txt RGList: dd$R: 'gProcessedSignal' dd$G: 'gMeanSignal' dd$Rb: 'gBGMedianSignal' dd$Gb: 'gBGUsed' >ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "vsn", + foreground = "MeanSignal", background = "BGMedianSignal", + offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE) BACKGROUND CORRECTION AND NORMALIZATION foreground: MeanSignal background: BGMedianSignal Array 1 corrected Array 2 corrected Array 3 corrected Array 4 corrected Error in normalizeBetweenArrays(ddBG$G, method = NORMmethod) : vsn method no longer supported. Please use normalizeVSN instead. >ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN", + foreground = "MeanSignal", background = "BGMedianSignal", + offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE) BACKGROUND CORRECTION AND NORMALIZATION Error in BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN", : NORMmethod should be one of 'none', 'quantile','vsn' >sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Agi4x44PreProcess_1.10.0 genefilter_1.32.0 annotate_1.28.1 AnnotationDbi_1.12.0 limma_3.6.9 [6] Biobase_2.10.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.9-4 splines_2.12.2 survival_2.36-5 xtable_1.5-6 Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_bioinfo.html http://staff.washington.edu/~dbeyer
vsn • 577 views
ADD COMMENTlink modified 8.4 years ago by Wolfgang Huber13k • written 8.4 years ago by Dick Beyer1.4k
Answer: Problem with BGandNorm() from the Agi4x44PreProcess package
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gravatar for Wolfgang Huber
8.4 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Hi Dick I have no specific understanding of this, but I would suggest trying with a current release of R (2.13) and Bioconductor (2.8), e.g. Agi4x44PreProcess 1.12.0 Best wishes Wolfgang Il May/6/11 8:20 PM, Dick Beyer ha scritto: > Hello, > > I've run into a problem that looks like the function BGandNorm() is broken because it relies on vsn as a method called by normalizeBetweenArrays, but that method has been replaced by a function normalizeVSN(). > > Here is some output that shows the problem: > >> dd<- read.AgilentFE(targets, makePLOT=FALSE) > Read US23502338_252643710125_S01_GE1_107_Sep09_1_4.txt > Read US23502338_252643710125_S01_GE1_107_Sep09_1_3.txt > Read US23502338_252643710125_S01_GE1_107_Sep09_1_2.txt > Read US23502338_252643710125_S01_GE1_107_Sep09_1_1.txt > > > RGList: > dd$R: 'gProcessedSignal' > dd$G: 'gMeanSignal' > dd$Rb: 'gBGMedianSignal' > dd$Gb: 'gBGUsed' > > >> ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "vsn", > + foreground = "MeanSignal", background = "BGMedianSignal", > + offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE) > BACKGROUND CORRECTION AND NORMALIZATION > > foreground: MeanSignal > background: BGMedianSignal > Array 1 corrected > Array 2 corrected > Array 3 corrected > Array 4 corrected > Error in normalizeBetweenArrays(ddBG$G, method = NORMmethod) : > vsn method no longer supported. Please use normalizeVSN instead. > > >> ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN", > + foreground = "MeanSignal", background = "BGMedianSignal", > + offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE) > BACKGROUND CORRECTION AND NORMALIZATION > > Error in BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN", : > NORMmethod should be one of 'none', 'quantile','vsn' > > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Agi4x44PreProcess_1.10.0 genefilter_1.32.0 annotate_1.28.1 AnnotationDbi_1.12.0 limma_3.6.9 > [6] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 RSQLite_0.9-4 splines_2.12.2 survival_2.36-5 xtable_1.5-6 > > Cheers, > Dick > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env.& Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/members_fc_bioinfo.html > http://staff.washington.edu/~dbeyer > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 8.4 years ago by Wolfgang Huber13k
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