May 2004 Archives by author

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Starting: Sat May 1 00:27:47 CEST 2004
Ending: Mon May 31 21:55:45 CEST 2004
Messages: 259

• [BioC] Normalization for different amts of RNA in limma   michael watson (IAH-C)
• [BioC] maNorm 2D   Vincent Carey 525-2265
• [BioC] training in bioconductor, boston, 28-29 june (2d announcement)   Vincent Carey 525-2265
• [BioC] Problem with mgu74av2LOCUSID environment   Fátima Núñez Mangado
• [BioC]: Chromosome plotting/geneplotter   Steffen Möller
• [BioC] Normalization for different amts of RNA in limma   Naomi Altman
• [BioC] Normalization of Intensities   Naomi Altman
• [BioC] tech reps revisited in limma   Naomi Altman
• [BioC] median polish vs mas   Naomi Altman
• [BioC] median polish vs mas   Naomi Altman
• [BioC] How to filter up- and down-regulated genes?   Naomi Altman
• [BioC] Un-balanced dye-swaps and LIMMA   Naomi Altman
• [BioC] Theoretical Question   Naomi Altman
• [BioC] RMA on PM only   Arne.Muller at aventis.com
• [BioC] comparing data frames   Arne.Muller at aventis.com
• [BioC] Probe level analysis   Arne.Muller at aventis.com
• [BioC] Drosophila GeneChip analysis   Arne.Muller at aventis.com
• [BioC] Drosophila GeneChip analysis   Arne.Muller at aventis.com
• [BioC] Problem with Loading Bioconductor 1.4 in Windows 2000   Karla Ballman
• [BioC] simpleaffy error for mouse4302cdf   Dick Beyer
• [BioC] Biobase or affy package makes update() not work   Dick Beyer
• [BioC] rma and gcrma do not work in R 1.9.0   Ben Bolstad
• [BioC] Chip art from affyPLM   Ben Bolstad
• [BioC] cdf vs probe package & Linux vs PC   Justin Borevitz
• [BioC] median polish vs mas/PLIER info   Anthony Bosco
• [BioC]: Chromosome plotting/geneplotter   Anthony Bosco
• [BioC] Resize plots to display axis labels   Anthony Bosco
• [BioC] error in gcrma background correction   Raffaele Calogero
• [BioC] loading exprSet from a file   Raffaele Calogero
• [BioC] Normalization for different amts of RNA in limma   Helen Cattan
• [BioC] help on reading cDNA   Lang Chen
• [BioC] How to use experimental data packages?   Tae-Hoon Chung
• [BioC] heatmap() customization   Sean Davis
• [BioC] How to filter up- and down-regulated genes?   Sean Davis
• [BioC]: Chromosome plotting/geneplotter   Sean Davis
• [BioC] supervised clustering   Marcel Dettling
• [BioC] boxplots: possible unexpected behavior   Ramon Diaz-Uriarte
• [BioC] ebayes and identifying outlyingly large variances   Ramon Diaz-Uriarte
• [BioC] differential expression, model selection and F-tests of nested models   Ramon Diaz-Uriarte
• [BioC] limma makeContrasts question   Luda Druskin
• [BioC] Problem with ReadAffy   Jose Duarte
• [BioC] library versions problem   Rob Dunne
• [BioC] Arabidosis annotation package   Jerzy Dyczkowski
• [BioC] Hierarchical clustering and shrinking centroids...   Tom R. Fahland
• [BioC] where to find the document of 'multtest.intro"   Fan, Wenhong
• [BioC] downstream analysis of differentially expressed genes   Fan, Wenhong
• [BioC] maNorm 2D   Matthew Fero
• [BioC] Interpretation of output of AffyRNAdeg and hist commands   Richard Friedman
• [BioC] Coordinates of streak   Richard Friedman
• [BioC] Display of histogram of RMA-processed data   Richard Friedman
• [BioC] Display of histogram of RMA-processed data   Richard Friedman
• [BioC] Display of histogram of RMA-processed data   Richard Friedman
• [BioC] Problem with obtaining annotation of mgu74av2 chip   Richard Friedman
• [BioC] where to find the document of 'multtest.intro"   Robert Gentleman
• [BioC] problem installing bioconductor   Jeff Gentry
• [BioC] Loading a file.tar.gz into R   Jeff Gentry
• [BioC] error handling in R   Jeff Gentry
• [BioC] makecdfenv not installed?   Jeff Gentry
• [BioC] Change to getBioC()   Jeff Gentry
• [BioC] "affy" installation problems   Jeff Gentry
• [BioC] problem with affy   Jeff Gentry
• [BioC] Release 1.4 - packages missing?   Jeff Gentry
• [BioC] Mailing list memberships   Jeff Gentry
• [BioC] bug in maNormMain ?   Jeff Gentry
• [BioC] Excel based software   Jeff Gentry
• [BioC] Installing Bioconductor 1.4 Help Files   Jeff Gentry
• [BioC] problem loading Rgraphviz library   Jeff Gentry
• [BioC] Rgraphviz installation problems   Jeff Gentry
• [BioC] maBoxplot in v1.4   Jeff Gentry
• [BioC] orphaned links   Jeff Gentry
• [BioC] maBoxplot in v1.4   Jeff Gentry
• [BioC] maBoxplot in v1.4   Jeff Gentry
• [BioC] Linking Rosetta gene accession numbers to GO terms   Goeman, J.J. (MSTAT)
• [BioC] external controls normalization   Ghislaine Guigon
• [BioC] problem loading Rgraphviz library   Rodrigo Gutierrez
• [BioC] Problem reading CEL files   Xia Han
• [BioC] Problem reading CEL files   Xia Han
• [BioC] Boxplot of RMA normalized data   Xia Han
• [BioC] (GC)RMA when there are BIG treatment effects.   Matthew Hannah
• [BioC] Un-balanced dye-swaps and LIMMA   Matthew Hannah
• [BioC] Un-balanced dye-swaps and LIMMA   Matthew Hannah
• [BioC] help with design matrix   Dennis Hazelett
• [BioC] how to remove unwanted spots from topTable output?   Dennis Hazelett
• [BioC] Re: limma t-tests and SAM   Dennis Hazelett
• [BioC] limma makeContrasts question   Stephen Henderson
• [BioC] paired comparisons with limma   Stephen Henderson
• [BioC] Hierarchical clustering and shrinking centroids...   Stephen Henderson
• [BioC] Fitting a contrast matrix in Limma   Laura Hollins
• [BioC] design matrix and lmFit problems in limma   pingzhao Hu
• [BioC] tissue contamination problem in microarray   Wolfgang Huber
• [BioC] Re: vsn error L-BFGS-B needs finite values of fn   Wolfgang Huber
• [BioC] Bioconductor 1.4 released   Wolfgang Huber
• [BioC] Normalization with common reference   Wolfgang Huber
• [BioC] Normalization with common reference   Wolfgang Huber
• [BioC] Rgraphviz installation problems   Jacob Hurst
• [BioC] Names of the samples (CEL file)   Rafael A. Irizarry
• [BioC] Display of histogram of RMA-processed data   Rafael A. Irizarry
• [BioC] median polish vs mas   Rafael A. Irizarry
• [BioC] problem installing bioconductor   V.C.L. de Jager
• [BioC] Limma package question   V.C.L. de Jager
• [BioC] number of Replicates - Fold change vs Limma or Siggenes/SAM   Nitin Jain
• [BioC] Bug in marray???   Joern Kamradt
• [BioC] Modifying marrayRaw requires marrayClasses ini BioC 1.4   Joern Kamradt
• [BioC] Modifying marrayRaw requires marrayClasses ini BioC 1.4   Joern Kamradt
• [BioC] problem with affy   Kaushik, Narendra K
• [BioC] limma spacing: intra- and inter- block replicates   Martin Kerick
• [BioC] limma 2x2 factorial experiment with two colour arrays, no common reference   Martin Kerick
• [BioC] affylmGUI   Simon Kidd
• [BioC] limma t-tests and SAM   Simon Kidd
• [BioC] Is rma in affylmGUI different to affy rma?   Simon Kidd
• [BioC] Is rma in affylmGUI different to affy rma?   Simon Kidd
• [BioC] error handling in R   Kimpel, Mark W
• [BioC] installation problems of affy package   Toralf Kirsten
• [BioC] Problem with PAM using R 1.9.0   Michelle Kittleson
• [BioC] Reading CEL file information   Vitalina Komashko
• [BioC] Names of the samples (CEL file)   Vitalina Komashko
• [BioC] Names of the samples(CEl file)(2)   Vitalina Komashko
• [BioC] How to filter up- and down-regulated genes?   Vitalina Komashko
• [BioC] How to filter up- and down-regulated genes?   Vitalina Komashko
• [BioC] Problem with updating Bioconductor   Vitalina Komashko
• [BioC] Doubt to set layout in limma   Marcelo Luiz de Laia
• [BioC] how to remove unwanted spots from topTable output?   Marcelo Luiz de Laia
• [BioC] orphaned links   Tom Laudeman
• [BioC] bug in maNormMain ?   Tarca Adi Laurentiu
• [BioC] makecdfenv not installed?   Martin Lercher
• [BioC] rma and gcrma do not work in R 1.9.0   Li, James [PRDUS Non-J&J]
• [BioC] import cDNA microarray data into R   Li, Jingyi
• [BioC] tissue contamination problem in microarray   Hao Liu
• [BioC] tissue contamination problem in microarray   Hao Liu
• [BioC] how to match matrix   Hao Liu
• [BioC] ANSI C not enforced intentionally?   Claudio Lottaz
• [BioC] Release 1.4 - packages missing?   Claudio Lottaz
• [BioC] Idenifying signatures across many samples?   Luckey, John
• [BioC] Theoretical Question   Luckey, John
• [BioC] number of Replicates - Fold change vs Limma or Siggenes/SAM   Luckey, John
• [BioC] gcrma in affylmGUI   Luckey, John
• [BioC] downstream analysis of differentially expressed genes   James MacDonald
• [BioC] GO and Annotation   James MacDonald
• [BioC] how build annotation package   James MacDonald
• [BioC] installation problems of affy package   James MacDonald
• [BioC] Loading a file.tar.gz into R   James MacDonald
• [BioC] Names of the samples(CEl file)(2)   James MacDonald
• [BioC] Interpretation of output of AffyRNAdeg and hist commands   James MacDonald
• [BioC] error handling in R   James MacDonald
• [BioC] Normalization for different amts of RNA in limma   James MacDonald
• [BioC] Display of histogram of RMA-processed data   James MacDonald
• [BioC] help error causing affy library install to fail   James MacDonald
• [BioC] median polish vs mas   James MacDonald
• [BioC] median polish vs mas   James MacDonald
• [BioC] iffail argument in mget of mas5, rma   James MacDonald
• [BioC] Re: tech reps revisited in limma (Naomi Altman)   James MacDonald
• [BioC] Mouse array   James MacDonald
• [BioC] Mouse array   Macchiarulo, Eugenio
• [BioC] Drosophila GeneChip analysis   Paul Mack
• [BioC] Limma 1.6.1 : composite normalisation method not recommended ?? (+ function error)   Laetitia Marisa
• [BioC] tech reps revisited in limma   Simon Melov
• [BioC] Re: tech reps revisited in limma (Naomi Altman)   Simon Melov
• [BioC] Error doing Mas5 calculation with Simpleaffy package   Crispin Miller
• [BioC] Error doing Mas5 calculation with Simpleaffy package   Crispin Miller
• [BioC] supervised clustering   Steve Moore
• [BioC] marrayClassaes   Maarten Morsink
• [BioC] "affy" installation problems   Tarun Nayar
• [BioC] Loading a file.tar.gz into R   Stephen Nyangoma
• [BioC] Loading a file.tar.gz into R   Stephen Nyangoma
• [BioC] tissue contamination problem in microarray   Oosting, J. (PATH)
• [BioC] Resize plots to display axis labels   Oosting, J. (PATH)
• [BioC] Binary CEL and CDF files   PARK,CHRISTOPHER CHANGSUN
• [BioC] Running justRMA on .CEL files in another directory   PARK,CHRISTOPHER CHANGSUN
• [BioC] supervised clustering   Park, Richard
• [BioC] Display of histogram of RMA-processed data   Lawrence-Paul Petalidis
• [BioC] using fitPLM weights in limma analysis   Tom Price
• [BioC] comparing data frames   Adaikalavan Ramasamy
• [BioC] Names of the samples (CEL file)   Adaikalavan Ramasamy
• [BioC] Error installing package affy   Adaikalavan Ramasamy
• [BioC] ReadAffy problem sampleNames + hgu95av2   Adaikalavan Ramasamy
• [BioC] ReadAffy problem sampleNames + hgu95av2   Adaikalavan Ramasamy
• [BioC] iffail argument in mget of mas5, rma   Adaikalavan Ramasamy
• [BioC] Running justRMA on .CEL files in another directory   Adaikalavan Ramasamy
• [BioC] MetaData broken links   James F. Reid
• [BioC] help error causing affy library install to fail   Roels, Steven
• [BioC] error handling in R   A.J. Rossini
• [BioC] ANSI C not enforced intentionally?   A.J. Rossini
• [BioC] Bioconductor 1.4 released   A.J. Rossini
• [BioC] Error doing Mas5 calculation with Simpleaffy package   Rudy.vanEijsden at GEN.unimaas.nl
• [BioC] Error doing Mas5 calculation with Simpleaffy package   Rudy.vanEijsden at GEN.unimaas.nl
• [BioC] how build annotation package   LIANHE SHAO
• [BioC] factdesign package   Denise Scholtens
• [BioC] factDesign - another question   Denise Scholtens
• [BioC] help with design matrix   Gordon Smyth
• [BioC] single channel in limma...   Gordon Smyth
• [BioC] Different results with limma on R 1.8.1 and R 1.9.0   Gordon Smyth
• [BioC] Fitting a contrast matrix in Limma   Gordon Smyth
• [BioC] Fitting a contrast matrix in Limma   Gordon Smyth
• [BioC] maNorm 2D   Floor Stam
• [BioC] comparing data frames   Straubhaar, Juerg
• [BioC] heatmap() customization   Straubhaar, Juerg
• [BioC] GO and Annotation   Mayte Suarez-Farinas
• [BioC] reading .gpr w/limma - error (bug??)   Mayte Suarez-Farinas
• [BioC] single channel in limma...   Mayte Suarez-Farinas
• [BioC] single channel analisis w/limma   Mayte Suarez-Farinas
• [BioC] Hierarchical clustering and shrinking centroids...   Tan, MinHan
• [BioC] Normalization for different amts of RNA in limma   Natalie P. Thorne
• [BioC] file format problem   Jose Gadea Vacas
• [BioC] gap-statistic implementation   Roel Verhaak
• [BioC] Different results with limma on R 1.8.1 and R 1.9.0   Dave Waddell
• [BioC] Re: affylmGUI figures estrogen data set   James Wettenhall
• [BioC] affylmGUI   James Wettenhall
• [BioC] affylmGUI   James Wettenhall
• [BioC] gcrma in affylmGUI   James Wettenhall
• [BioC] limmaGUI & affylmGUI wizards for Windows & bug fixes   James Wettenhall
• [BioC] gcrma in affylmGUI   James Wettenhall
• [BioC] Installing Bioconductor 1.4 Help Files   White, Charles E WRAIR-Wash DC
• [BioC] Installing Bioconductor 1.4 Help Files   White, Charles E WRAIR-Wash DC
• [BioC] factdesign package   Claire Wilson
• [BioC] factDesign - another question   Claire Wilson
• [BioC] pamr.from.excel   Willy Wynant
• [BioC] pamr.from.excel problem   Willy Wynant
• [BioC] Bug in marray???   Jean Yee Hwa Yang
• [BioC] import cDNA microarray data into R   Jean Yee Hwa Yang
• [BioC] marrayClassaes   Jean Yee Hwa Yang
• [BioC] Modifying marrayRaw requires marrayClasses ini BioC 1.4   Jean Yee Hwa Yang
• [BioC] maBoxplot in v1.4   Jean Yee Hwa Yang
• [BioC] normalization   Jean Yee Hwa Yang
• [BioC] Limma package question   John S. Yordy
• [BioC] GO and Annotation   John Zhang
• [BioC] comparing data frames   John Zhang
• [BioC] Problem with mgu74av2LOCUSID environment   John Zhang
• [BioC] how build annotation package   John Zhang
• [BioC] Linking Rosetta gene accession numbers to GO terms   John Zhang
• [BioC] A simple question   John Zhang
• [BioC] Re: MetaData 1.6.0   John Zhang
• [BioC] How to create customized probe package for GCRMA?   Kun Zhang
• [BioC] A simple question   Ainong Zhou
• [BioC] A summary of answers to get affyid from locusid   Ainong Zhou
• [BioC] maBoxplot in v1.4   charles.edwin.white at us.army.mil
• [BioC] Running justRMA on .CEL files in another directory   donghu at itsa.ucsf.edu
• [BioC] geneplotter and base position   david neil hayes
• [BioC] question about plot dendrogram   ivan.borozan at utoronto.ca
• [BioC] multtest data preprocessing questions   ulas karaoz
• [BioC] multtest data preprocessing questions   ulas karaoz
• [BioC] tissue contamination problem in microarray   lgautier at altern.org
• [BioC] Biobase or affy package makes update() not work   lgautier at altern.org
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Time course in BioC   marchiem at libero.it
• [BioC] Normalization with common reference   marchiem at libero.it
• [BioC] Re: Welcome to the "Bioconductor" mailing list   mkmarket at runbox.com
• [BioC] Problem in connecting R with internet   rashi
• [BioC] Statistics::R   peter robinson
• [BioC] Statistics::R   peter robinson
• [BioC] problem installing bioconductor   vjager
• [BioC] cdf vs probe package & Linux vs PC   w.huber at dkfz-heidelberg.de
• [BioC] Problem with plot   witek
• [BioC] normalization   xpzhang
• [BioC] is my normalization right?   xpzhang
• [BioC] test   xpzhang

Last message date: Mon May 31 21:55:45 CEST 2004
Archived on: Tue Jun 1 15:59:04 CEST 2004

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