July 2004 Archives by date

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Starting: Thu Jul 1 01:00:57 CEST 2004
Ending: Sat Jul 31 13:07:06 CEST 2004
Messages: 341

• [BioC] Error with read.imagene   Gordon Smyth
• [BioC] limma_design_matrix.   Gordon Smyth
• [BioC] different results from limma using the same data set and two different methods   xiaocui zhu
• [BioC] different results from limma using the same data set and two different methods   Gordon Smyth
• [BioC] Error: read.affybatch   S Peri
• [BioC] Error: read.affybatch   S Peri
• [BioC] Re: B statistic (was: affylmGUI exporting)   James Wettenhall
• [BioC] Error: read.affybatch   S Peri
• [BioC] Error: read.affybatch   Ben Bolstad
• [BioC] "limma" and "Imagene"   Breuk102
• [BioC] "limma" and "Imagene"   James Wettenhall
• [BioC] Error: expresso   S Peri
• [BioC] Error: read.affybatch   Adaikalavan Ramasamy
• [BioC] Error: expresso   James MacDonald
• [BioC] New gene expression scanner   James MacDonald
• [BioC] Questions related to processing large dataset in batches   James MacDonald
• [BioC] Removing bad flag spot using marray   Julien Bauer
• [BioC] simpleaffy error   kfbargad at lg.ehu.es
• [BioC] simpleaffy error   James MacDonald
• [BioC] Error in La.chol(t(A/s)/s) fitting limma models   Paul Boutros
• [BioC] "limma" and "Imagene"   Gordon Smyth
• [BioC] simpleaffy error   kfbargad at lg.ehu.es
• [BioC] simpleaffy error   Crispin Miller
• [BioC] simpleaffy error   Crispin Miller
• [BioC] limmaGUI_1.2.5 ImaGene fix   James Wettenhall
• [BioC] mtry in randomForest   Liu, Xin
• [BioC] LimmaGUI Spot Quality   Elizabeth Brooke-Powell
• [BioC] LimmaGUI Spot Quality   James Wettenhall
• [BioC] LimmaGUI Spot Quality   Elizabeth Brooke-Powell
• [BioC] mtry in randomForest   Liaw, Andy
• [BioC] simpleaffy error   James MacDonald
• [BioC] recipe for heatmap   Marc Salit
• [BioC] recipe for heatmap   Sean Davis
• [BioC] recipe for heatmap   Laura Hollins
• [BioC] rpart - stack overflow   Liu, Xin
• [BioC] LimmaGUI Spot Quality   James Wettenhall
• [BioC] LimmaGUI Spot Quality   Elizabeth Brooke-Powell
• [BioC] getBioC("affy")   Lana Schaffer
• [BioC] LimmaGUI Spot Quality   Gordon Smyth
• [BioC] a custom CDF file   Lana Schaffer
• [BioC] a custom CDF file   James MacDonald
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] LimmaGUI Spot Quality   Gordon Smyth
• [BioC] [limma] Interpreting B and P values   Marcelo Luiz de Laia
• [BioC] simpleaffy error   kfbargad at lg.ehu.es
• [BioC] simpleaffy error   kfbargad at lg.ehu.es
• [BioC] LIMMA and write.fit   S_Thieme
• [BioC] XML data   S Peri
• [BioC] XML data   Sean Davis
• [BioC] unlist changes the length?   Irene Li
• [BioC] unlist changes the length?   Robert Gentleman
• [BioC] dye-swap and arrayMagic   Dr_Gyorffy_Balazs
• [BioC] Mailing Lists: Timeout today GMT 18--19.30   Martin Maechler
• [BioC] dye-swap and arrayMagic   michael watson (IAH-C)
• [BioC] dye-swap and arrayMagic   Andreas Buness
• [BioC] OT: cell lines and tissues   Ghai, Rohit
• [BioC] OT: cell lines and tissues   Stefano Calza
• [BioC] pamr and sample.subset option   Dr_Gyorffy_Balazs
• [BioC] marray error message   Dr_Gyorffy_Balazs
• [BioC] SAM - survival analysis   Willy Wynant
• [BioC] SAM - survival analysis   Holger Schwender
• [BioC] OT: cell lines and tissues   Stefano Calza
• [BioC] OT: cell lines and tissues   Dapeng Cui
• [BioC] OT: cell lines and tissues   Rohit Ghai
• [BioC] Questions on arrayQuality   Richard Friedman
• [BioC] problem with expresso(...normalize.method="vsn")   Stefano Calza
• [BioC] Questions on arrayQuality   Paquet, Agnes
• [BioC] read.frame   S Peri
• [BioC] Statistics for Diagnostic Microarrays   michael watson (IAH-C)
• [BioC] Statistics for Diagnostic Microarrays   Adaikalavan Ramasamy
• [BioC] Statistics for Diagnostic Microarrays   michael watson (IAH-C)
• [BioC] Statistics for Diagnostic Microarrays   michael watson (IAH-C)
• [BioC] Statistics for Diagnostic Microarrays   A.J. Rossini
• [BioC] Statistics for Diagnostic Microarrays   michael watson (IAH-C)
• [BioC] Statistics for Diagnostic Microarrays   Adaikalavan Ramasamy
• [BioC] Statistics for Diagnostic Microarrays   A.J. Rossini
• [BioC] Any problems with R 1.9.1?   Jenny Drnevich
• [BioC] Question regarding bg correction/normalization/summarization   Tova Fuller
• [BioC] help   Michael Stapelberg
• [BioC] Control spots for global normalization   thama at imbb.forth.gr
• [BioC] RE: Any problems with R 1.9.1?   Chang, Kai-Ming
• [BioC] Control spots for global normalization   Christian Landry
• [BioC] limma question   Thomas Schlitt
• [BioC] help   James MacDonald
• [BioC] RE: Any problems with R 1.9.1?   Jenny Drnevich
• [BioC] OT: cell lines and tissues   YUK FAI LEUNG
• [BioC] makecdfenv   Lana Schaffer
• [BioC] makecdfenv   James MacDonald
• [BioC] affymetrix zebrafish chip   YUK FAI LEUNG
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Question regarding bg correction/normalization/summarization   Wolfgang Huber
• [BioC] affymetrix zebrafish chip   James MacDonald
• [BioC] Citing R / Bioconductor   Tan, MinHan
• [BioC] limma question   James Wettenhall
• [BioC] Suggestion for affycomp   Hinrich Göhlmann
• [BioC] help   James Wettenhall
• [BioC] (no subject)   Mayte Suarez-Farinas
• [BioC] (no subject)   John Zhang
• [BioC] screening for array outliers   Kimpel, Mark W
• [BioC] problem (bug?) and solution for pm function   Jenny Drnevich
• [BioC] problem (bug?) and solution for pm function   Rafael A. Irizarry
• [BioC] problem (bug?) and solution for pm function   Jenny Drnevich
• [BioC] number of affy-chips needed to fit rma model   Dipl.-Ing. Johannes Rainer
• [BioC] number of affy-chips needed to fit rma model   Rafael A. Irizarry
• [BioC] how to reduce the file size of scatter plot matrix   Caimiao Wei
• [BioC] makecdfenv()   Lana Schaffer
• [BioC] makecdfenv()   Robert Gentleman
• [BioC] limma question   Gordon K Smyth
• [BioC] how to reduce the file size of scatter plot matrix   A.J. Rossini
• [BioC] how to reduce the file size of scatter plot matrix   James Wettenhall
• [BioC] limma and composite normalization method   Diego Díez Ruiz
• [BioC] Comparison of correlation coefficients   Christian.Stratowa at vie.boehringer-ingelheim.com
• [BioC] Two questions about image() function in Affy package   F Duan
• [BioC] Difference between normalizeWithinArrays and stat.ma   Saroj Mohapatra
• [BioC] Difference between normalizeWithinArrays and stat.ma   Saroj Mohapatra
• [BioC] affy, how to define the normalization method that works with my data   Dipl.-Ing. Johannes Rainer
• [BioC] Limma and Dye-Swap/Single Channel   S_Thieme
• [BioC] affy package in MacOSX   Tiago R Magalhaes
• [BioC] how to reduce the file size of scatter plot matrix   Michael Seewald
• [BioC] Limma and Dye-Swap/Single Channel   Naomi Altman
• [BioC] how to reduce the file size of scatter plot matrix   Wolfgang Huber
• [BioC] how to reduce the file size of scatter plot matrix   Wolfgang Huber
• [BioC] how to reduce the file size of scatter plot matrix   F Duan
• [BioC] what normalization method does mas5 use   Brian Bennett
• [BioC] what normalization method does mas5 use   F Duan
• [BioC] what normalization method does mas5 use   James MacDonald
• [BioC] what normalization method does mas5 use   F Duan
• [BioC] limma   Peter Wilkinson
• FW: [BioC] makecdfenv()   Lana Schaffer
• [BioC] Making alternative CDF enviroments   Mario Caceres
• [BioC] affy package in MacOSX   James Wettenhall
• [BioC] Difference between normalizeWithinArrays and stat.ma   Gordon K Smyth
• [BioC] Limma and Dye-Swap/Single Channel   Gordon K Smyth
• [BioC] Making alternative CDF enviroments   Laurent Gautier
• [BioC] limma   James MacDonald
• [BioC] Methods to combine U133A and B?   Simon Lin
• [BioC] 2x3 ANOVA   Jeff Lande
• [BioC] Methods to combine U133A and B?   Adaikalavan Ramasamy
• Fwd: Re: [BioC] 2x3 ANOVA   Denise Scholtens
• [BioC] How to read flag info from ImaGene output file   Saroj Mohapatra
• [BioC] problems in makecdfenv with affy custom resequencing arrays   Vishal Berry
• [BioC] limma   Peter Wilkinson
• [BioC] limma   Kasper Daniel Hansen
• [BioC] 2x3 ANOVA   Jeff Lande
• [BioC] limma   James Wettenhall
• [BioC] How to read flag info from ImaGene output file   James Wettenhall
• [BioC] limma and composite normalization method   Gordon K Smyth
• [BioC] limma   Gordon K Smyth
• [BioC] Re: How to read flag info from ImaGene output file   Gordon K Smyth
• [BioC] limma   Peter Wilkinson
• [BioC] rma on affy experiment with different cell lines   Dipl.-Ing. Johannes Rainer
• [BioC] Bayesian selection of genes and its correct template   Ian Jeffery
• [BioC] rma on affy experiment with different cell lines   James MacDonald
• [BioC] detection vs. detection of change   John Welsh
• [BioC] detection vs. detection of change   A.J. Rossini
• [BioC] gcrma   Rafael A. Irizarry
• [BioC] searchable mail archives - updated   Istvan Albert
• [BioC] 64 Bit Itanium and the Affy Package   larsenmtl at comcast.net
• [BioC] RG-to-MA transformation in protein arrays   Saroj Mohapatra
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] (no subject)   giuseppe scarsi
• [BioC] cant draw GO graph labels   Michael Pheasant
• [BioC] cant draw GO graph labels   Jeff Gentry
• [BioC] Bayesian selection of genes and its correct template   Gordon Smyth
• [BioC] Re: Suggestion for affycomp   Hinrich Göhlmann
• [BioC] boxplot(affybatch)   Matthew Hannah
• [BioC] Comparison of correlation coefficients - Details   Christian.Stratowa at vie.boehringer-ingelheim.com
• [BioC] Normalising divergent samples - Discussion (Please!)   Matthew Hannah
• [BioC] boxplot(affybatch)   James MacDonald
• [BioC] Bayesian method in limma   Hua Weng
• [BioC] Re: Suggestion for affycomp   Rafael A. Irizarry
• [BioC] gcrma.bg.transformation missing in gcrma 1.1.0   Jeffrey Rasmussen
• [BioC] short time-course design. Any suggestion?   Stefano Calza
• [BioC] Re: [R] An image() problem related to Affy package in BioC   Adaikalavan Ramasamy
• [BioC] VSN combined with RMA   Remo Sanges
• [BioC] How to save affybatch objects   Yihuan Xu
• [BioC] Normalization analyzing different strains   Remo Sanges
• [BioC] VSN combined with RMA   Rafael Irizarry
• [BioC] How to save affybatch objects   Kasper Daniel Hansen
• [BioC] Bayesian method in limma   Gordon Smyth
• [BioC] short time-course design. Any suggestion?   Matthew Hannah
• [BioC] heatmaps and pearson correlation   Arne.Muller at aventis.com
• [BioC] heatmaps and pearson correlation   michael watson (IAH-C)
• [BioC] heatmaps and pearson correlation   Wolski
• [BioC] pooling paper   Rafael A. Irizarry
• [BioC] short time-course design. Any suggestion?   Naomi Altman
• [BioC] short time-course design. Any suggestion?   Adaikalavan Ramasamy
• [BioC] GCRMA 1.0.0 vs 1.1.0   Caimiao Wei
• [BioC] New Alzheimer's disease microarray data set available   Eric
• [BioC] RDBIPgSQL: strange inheritance problems   Dipl.-Ing. Johannes Rainer
• [BioC] heatmaps and pearson correlation   Arne.Muller at aventis.com
• [BioC] heatmaps and pearson correlation   Wolfgang Huber
• [BioC] Am I using limma incorrectly?   michael watson (IAH-C)
• [BioC] How to use datapackage homology   Claudio Lottaz
• [BioC] Am I using limma incorrectly?   Gordon K Smyth
• [BioC] Normalising divergent samples - Discussion (Please!)   Matthew Hannah
• [BioC] RE: Comparison of correlation coefficients - Details   Christian.Stratowa at vie.boehringer-ingelheim.com
• [BioC] RdbiPgSQL: any possibility to check for errors?   Dipl.-Ing. Johannes Rainer
• [BioC] short time-course design. Any suggestion?   Stefano Calza
• [BioC] RDBIPgSQL: strange inheritance problems   John Zhang
• [BioC] How to use datapackage homology   John Zhang
• [BioC] How to use datapackage homology   Robert Gentleman
• [BioC] RDBIPgSQL: strange inheritance problems   Dipl.-Ing. Johannes Rainer
• [BioC] Limma read.maimages generic import   Peter Wilkinson
• [BioC] multiple comparisons followed by multiple tests   Richard Friedman
• [BioC] multiple comparisons followed by multiple tests   Matthew Hannah
• [BioC] multiple comparisons followed by multiple tests   Richard Friedman
• [BioC] GCRMA backgrounds?   Andrew Harrison
• [BioC] proposal to modify Limma read.maimages generic import   Peter Wilkinson
• [BioC] Re: [R] RE: Comparison of correlation coefficients - Details   idimakos at upatras.gr
• [BioC] limma   daniela.marconi at libero.it
• [BioC] Re:limma   daniela.marconi at libero.it
• [BioC] multiple comparisons followed by multiple tests   Matthew Hannah
• [BioC] Replicates within array   Hua Weng
• [BioC] GCRMA backgrounds?   Matthew Hannah
• [BioC] split.AffyBatch   Wenbin Liu
• [BioC] GCRMA backgrounds?   Michael Barnes
• [BioC] split.AffyBatch   F Duan
• [BioC] split.AffyBatch   James MacDonald
• [BioC] Question   jcurry at vbi.vt.edu
• [BioC] [Fwd: Question]   jcurry at vbi.vt.edu
• [BioC] Question   James MacDonald
• [BioC] GCRMA backgrounds?   Zhijin Wu
• [BioC] proposal to modify Limma read.maimages generic import   Gordon Smyth
• [BioC] GCRMA backgrounds?   Matthew Hannah
• [BioC] limmaGUI and Agilent output files!   Adrian Peres
• [BioC] short time-course design. Any suggestion?   Stefano Calza
• [BioC] RE: [R] RE: Comparison of correlation coefficients - Details   Christian.Stratowa at vie.boehringer-ingelheim.com
• [BioC] split.AffyBatch   James MacDonald
• [BioC] split.AffyBatch   Laurent Gautier
• [BioC] Re: Bioconductor Digest, Vol 17, Issue 17   Raoul-Sam Daruwala
• probe length was:RE: [BioC] GCRMA backgrounds?   Michael Barnes
• probe length was:RE: [BioC] GCRMA backgrounds?   A.J. Rossini
• [BioC] repos tools   peter
• [BioC] limmaGUI and Agilent output files!   James Wettenhall
• [BioC] split.AffyBatch   Laurent Gautier
• [BioC] Problem with genRepos function in reposTools package   Valtteri Wirta
• [BioC] Re: limmaGUI and Agilent output files!   Elizabeth Brooke-Powell
• [BioC] problems with pm.getabst   Max_Kuhn at bd.com
• [BioC] probe length was:RE: [BioC] GCRMA backgrounds?   paul.boutros at utoronto.ca
• [BioC] MAS5 and Loess normalization   Arne.Muller at aventis.com
• [BioC] problems with pm.getabst   Max_Kuhn at bd.com
• [BioC] RNA degradation plots   kfbargad at lg.ehu.es
• [BioC] Affymetrix cdf-package question   Tae-Hoon Chung
• [BioC] Affymetrix cdf-package question   Jeff Gentry
• [BioC] RNA degradation plots   James MacDonald
• [BioC] PlotMA   Hao Liu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] read.frame   Naomi Altman
• [BioC] Plotting together data from hgu133a and b   Raffaele Calogero
• [BioC] Plotting together data from hgu133a and b   Robert Gentleman
• [BioC] Affymetrix cdf-package question   Laurent Gautier
• [BioC] problem dwnloading GOstats   Harry Hurd
• [BioC] problem dwnloading GOstats   Robert Gentleman
• [BioC] problem with reposTools link in getBioC?   Michael Janis
• [BioC] 2x2 factorial design in limma   Kimpel, Mark W
• [BioC] probe length was:RE: [BioC] GCRMA backgrounds?   Paul Boutros
• [BioC] Top 50 Candidate genes: "wrong" pValues and B results!   Adrian Peres
• [BioC] LIMMA: normalizeBetweenArrays   S_Thieme
• [BioC] M box Plot results-do they look OK?   Adrian Peres
• [BioC] expresso question   Marcus Albrecht
• [BioC] LimmaGUI spot type files   Elizabeth Brooke-Powell
• [BioC] pearson correlation.   Dixon, Dr R.
• [BioC] pearson correlation   Dixon, Dr R.
• [BioC] pearson correlation.   Heidi Dvinge
• [BioC] pearson correlation.   Steffen Durinck
• [BioC] Top 50 Candidate genes: "wrong" pValues and B results!   James MacDonald
• [BioC] PlotMA   James MacDonald
• [BioC] Agilent microarray   s-uchida
• [BioC] Limma design matrix   Yihuan Xu
• [BioC] Top 50 Candidate genes: "wrong" pValues and B results!   Gordon Smyth
• [BioC] LIMMA: normalizeBetweenArrays   Gordon Smyth
• [BioC] Limma design matrix   Gordon Smyth
• [BioC] Non-conformable arguments fitting limma contrasts   paul.boutros at utoronto.ca
• [BioC] pearson correlation.   Laurent Gautier
• [BioC] Affymetrix quality control and normalization   Dipl.-Ing. Johannes Rainer
• [BioC] LimmaGUI spot type files   Gordon Smyth
• [BioC] LimmaGUI spot type files   James Wettenhall
• [BioC] LimmaGUI spot type files   Elizabeth Brooke-Powell
• [BioC] LimmaGUI spot type files   Gordon Smyth
• [BioC] Affymetrix quality control and normalization   laurent buffat
• [BioC] Normalization with cDNA microarray Control Spot / limma   Sek Won Kong,M.D
• [BioC] KNN, SVM, and randomForest - How to predict samples without category   Liu, Xin
• [BioC] geneFilter - filter out gene probe set?   Liu, Xin
• [BioC] 2-colour cDNA data quality (+different species)   Matthew Hannah
• [BioC] Multiple testing correction on 2-Way ANOVA   Eric
• [BioC] KNN, SVM, and randomForest - How to predict samples without category   Tom R. Fahland
• [BioC] Multiple testing correction on 2-Way ANOVA   Liaw, Andy
• [BioC] Multiple testing correction on 2-Way ANOVA   Eric
• [BioC] gcrma 'type' default   Karen Vranizan
• [BioC] Normalization with cDNA microarray Control Spot / limma   Gordon Smyth
• [BioC] Multiple testing correction on 2-Way ANOVA   Adaikalavan Ramasamy
• [BioC] Non-conformable arguments fitting limma contrasts   Gordon Smyth
• [BioC] Non-conformable arguments fitting limma contrasts   Paul Boutros
• [BioC] How to download package bundles?   Peter Baker (CMIS, St Lucia)
• [BioC] KNN, SVM, and randomForest - How to predict test without known categories   Liu, Xin
• [BioC] Non-conformable arguments fitting limma contrasts   Gordon Smyth
• [BioC] KNN, SVM, and randomForest - How to predict test without known categories   Sean Davis
• [BioC] KNN, SVM, and randomForest - How to predict test without known categories (affy data)   Liu, Xin
• [BioC] gcrma 'type' default   James MacDonald
• [BioC] KNN, SVM, and randomForest - How to predict test without known categories   Adaikalavan Ramasamy
• [BioC] KNN, SVM, and randomForest - How to predict testing set without known categories (affy data)   Liu, Xin
• [BioC] Re: KNN, SVM, and randomForest - How to predict testing set without known categories (affy data)   Adaikalavan Ramasamy
• [BioC] Re: KNN, SVM, and randomForest - How to predict testing set without known categories (affy data)   Kasper Daniel Hansen
• [BioC] accessing affy library   Matthew Hahn
• [BioC] pamr Error: each class must have >1 sample   Dick Beyer
• [BioC] normalisation for universal reference in 2 channel arrays   Peter Wilkinson
• [BioC] Non-conformable arguments fitting limma contrasts   Kasper Daniel Hansen
• [BioC] pamr Error: each class must have >1 sample   Kasper Daniel Hansen
• [BioC] pamr Error: each class must have >1 sample   Dick Beyer
• [BioC] pamr Error: each class must have >1 sample   Kasper Daniel Hansen
• [BioC] normalisation for universal reference in 2 channel arrays   Gordon Smyth
• [BioC] pamr Error: each class must have >1 sample   Dick Beyer
• [BioC] RMA with biological replicates   Dipl.-Ing. Johannes Rainer
• [BioC] RMA with biological replicates   Dipl.-Ing. Johannes Rainer
• [BioC] RMA with biological replicates   Adaikalavan Ramasamy
• [BioC] RMA with biological replicates   James MacDonald
• [BioC] 2-colour bias AFTER normalising with Limma, labelling QC   Matthew Hannah
• [BioC] 2-colour bias AFTER normalising with Limma, labelling QC   Sean Davis
• [BioC] 2-colour bias AFTER normalising with Limma, labelling QC   Matthew Hannah
• [BioC] RMA with biological replicates   Naomi Altman
• [BioC] Image analysis for single channel macro arrays   Nicholas Lewin-Koh
• [BioC] Image analysis for single channel macro arrays   Peter Wilkinson
• [BioC] Image analysis for single channel macro arrays   Nicholas Lewin-Koh
• [BioC] Image analysis for single channel macro arrays   James Wettenhall
• [BioC] Image analysis for single channel macro arrays   Nicholas Lewin-Koh
• [BioC] RMA with biological replicates   Dipl.-Ing. Johannes Rainer
• [BioC] sort the difference and save to individual files problem   Dr_Gyorffy_Balazs
• [BioC] sort the difference and save to individual files problem   Adaikalavan Ramasamy
• [BioC] sort the difference and save to individual files problem   Adaikalavan Ramasamy
• [BioC] problem with MOE430a annotation & NetAffx correspondence   Stefano Calza
• [BioC] FW: [BiO News] Gene name errors introduced by Excel   Lapointe, David
• [BioC] problem with MOE430a annotation & NetAffx correspondence   John Zhang
• [BioC] GOstats:   Simon Lin
• [BioC] question about the error from function intraspotCorrelation   Ren Na
• [BioC] GOstats:   John Zhang
• [BioC] problem with MOE430a annotation & NetAffx correspondence   John Zhang
• [BioC] GOstats: another problem   Simon Lin
• [BioC] GOstats: another problem   James MacDonald
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] question about the error from function intraspotCorrelation   Gordon Smyth

Last message date: Sat Jul 31 13:07:06 CEST 2004
Archived on: Sat Jul 31 13:07:16 CEST 2004

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