April 2004 Archives by date

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Starting: Thu Apr 1 00:01:38 CEST 2004
Ending: Fri Apr 30 22:07:27 CEST 2004
Messages: 277

• [BioC] CELfiles names in a matrix   James MacDonald
• [BioC] Different levels of replicates and how to create a correct targets file out of that.   Naomi Altman
• [BioC] Problems in limma package   Gordon Smyth
• [BioC] Re: technical replicates (again!): a summary   Gordon Smyth
• [BioC] Factorial design with LIMMA   cmprobst
• [BioC] Factorial design with LIMMA   Gordon Smyth
• [BioC] Factorial design with LIMMA   cmprobst
• [BioC] Problems installing affy package.   Debjani Bhowmick
• [BioC] Different levels of replicates and how to create a correct targets file out of that.   Gordon Smyth
• [BioC] Re: technical replicates (again!): a summary   Johan Lindberg
• [BioC] Class discovery options?   paul.boutros at utoronto.ca
• [BioC] technical replicates (again!): a summary   Ramon Diaz-Uriarte
• [BioC] Re: technical replicates (again!): a summary   Ramon Diaz-Uriarte
• [BioC] Re: technical replicates (again!): a summary   Ramon Diaz-Uriarte
• [BioC] Questions on finding DE genes by Limma   rwin qian
• [BioC] Re: technical replicates (again!): a summary   Naomi Altman
• [BioC] citation for AnnAffy?   Patrick Cahan
• [BioC] Classification question   Tom R. Fahland
• [BioC] gcrma and new Affy IVT/hyb protocol   Anthony Bosco
• [BioC] gcrma and new Affy IVT/hyb protocol   Rafael A. Irizarry
• [BioC] RMA   pingzhao Hu
• Fwd: Re: [BioC] Different levels of replicates and how to create a correct targets file out of that.   Johan Lindberg
• [BioC] problems with RdbiPgSQL package   javier garcia - CEBAS
• [BioC] limma question   ivan.borozan at utoronto.ca
• [BioC] marrayInput: different gal files for the same experiment   Scott Rifkin
• [BioC] simpleaffy   Simon Kidd
• [BioC] Advantages of gcrma over rma?   Simon Kidd
• [BioC] limma question   James Wettenhall
• [BioC] limma question   Gordon Smyth
• [BioC] Re: [R] marrayNorm package (fwd)   anthony.ferrari at ensimag.imag.fr
• [BioC] no codes for the screenshots?   Robert Gentleman
• [BioC] Cannot find hgu133aprobe package   Eric
• [BioC] Cannot find hgu133aprobe package   Stephen Henderson
• [BioC] marrayInput: different gal files for the same experiment   Jean Yee Hwa Yang
• [BioC] Cannot find hgu133aprobe package   Aedin
• [BioC] no codes for the screenshots?   Ming Chen
• [BioC] help with packages   Alberto Goldoni
• [BioC] simpleaffy   Rudy.vanEijsden at GEN.unimaas.nl
• [BioC] Background correction - limma   Helen Cattan
• [BioC] memory usage ReadAffy() and probe level information   Roel Verhaak
• [BioC] memory usage ReadAffy() and probe level information   James MacDonald
• [BioC] memory usage ReadAffy() and probe level information   Arne.Muller at aventis.com
• [BioC] memory usage ReadAffy() and probe level information   Tan, MinHan
• [BioC] rma() error   Jose Duarte
• [BioC] help with packages   Jeff Gentry
• [BioC] help with packages   asemeria at cramont.it
• [BioC] Opinions on LIMaS   Stan Smiley
• [BioC] robust linear model in anovas   Arne.Muller at aventis.com
• [BioC] help with packages   Steffen Möller
• [BioC] Background correction - limma   Gordon Smyth
• FW: [BioC] Re: [R] marrayNorm package (fwd)   Jean Yee Hwa Yang
• [BioC] Design in factDesign   Jordi Altirriba Gutiérrez
• [BioC] limma and nested factors   Arne.Muller at aventis.com
• [BioC] version information   Obi Griffith
• [BioC] version information   James MacDonald
• [BioC] Limma   Seby
• [BioC] Limma   James MacDonald
• [BioC] limma reading genpix files   Bryce MacIver
• [BioC] limma and nested factors   Gordon Smyth
• [BioC] justGCRMA: Argument is missing, with no default   Dick Beyer
• [BioC] AFFY PLIER ALGORITHM   Anthony Bosco
• [BioC] Limma   Matthew Hannah
• [BioC] Array Comparative genome hybridization (CGH) linked to gene expression micro-arrays   Dr. Dirk Hasenclever
• [BioC] justGCRMA: Argument is missing, with no default   James MacDonald
• [BioC] limma and nested factors   Stephen Henderson
• [BioC] limma and nested factors   Arne.Muller at aventis.com
• [BioC] limma reading genpix files   Heidi Dvinge
• [altirriba@hotmail.com: [BioC] Design in factDesign] (fwd)   Denise Scholtens
• [BioC] ImaGene data into limma   Heidi Dvinge
• [BioC] justGCRMA: Argument is missing, with no default   Dick Beyer
• [BioC] Help in analysis   Marcelo Luiz de Laia
• [BioC] possible change   Rafael A. Irizarry
• [BioC] phenoData   Simon Kidd
• [BioC] phenoData   John Zhang
• [altirriba@hotmail.com: [BioC] Design in factDesign] (fwd)   Jordi Altirriba Gutiérrez
• [BioC] phenoData   James MacDonald
• [BioC] ImaGene data into limma   Gordon K Smyth
• [BioC] limma reading genpix files   Gordon K Smyth
• [BioC] GO problems with annaffy   Paolo Sirabella
• [altirriba@hotmail.com: [BioC] Design in factDesign] (fwd)   Kasper Daniel Hansen
• [BioC] limma--lm.fit and lm.series   PW Tsai
• [BioC] GO problems with annaffy   Jose Duarte
• [BioC] bioconductor keywords?   Mirka Zednikova
• [BioC] phenoData   Simon Kidd
• [BioC] rlm function   SERGI VIVES CIVIT
• [BioC] Boston Bioconductor Training Course Dates: 28-29 June 2004   Vincent Carey 525-2265
• [BioC] gcrma.1.0.0 vs gcrma.1.0.6 vs justGCRMA.1.0.6   Dick Beyer
• [BioC] gcrma.1.0.0 vs gcrma.1.0.6 vs justGCRMA.1.0.6   James MacDonald
• [BioC] gcrma.bg.transformation missing in gcrma 1.0.6   Dick Beyer
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [altirriba@hotmail.com: [BioC] Design in factDesign] (fwd)   Denise Scholtens
• [BioC] simpleaffy qc.stats error on mouse4302 arrays   Dick Beyer
• [BioC] Help with justRMA in affy package   PARK,CHRISTOPHER CHANGSUN
• [BioC] [PATCH] apparent bug in RdbiPgSQL (logicals always false)   Mitchell Skinner
• [BioC] help with genefinder/geneplotter   Anthony Bosco
• [altirriba@hotmail.com: [BioC] Design in factDesign] (fwd)   Jordi Altirriba Gutiérrez
• [BioC] simpleaffy qc.stats error on mouse4302 arrays   Michael
• [BioC] Reading SMD datasets   Stanley M Dunn
• [BioC] Help with justRMA in affy package   James MacDonald
• [BioC] [PATCH] apparent bug in RdbiPgSQL (logicals always false)   John Zhang
• [BioC] RMA vignette   Baker, Stephen
• [BioC] RMA vignette   Aedin
• [BioC] RMA vignette   A.J. Rossini
• [BioC] Problems with rma/justRMA and gcrma/justGCRMA   James MacDonald
• [BioC] limma reading genpix files   David Nelson
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Marc Salit
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9y   Kasper Daniel Hansen
• [BioC] limma reading genpix files   Gordon Smyth
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Simon Kidd
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Anthony Bosco
• [BioC] Problem installing Rgraphviz   Nicholas Lewin-Koh
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   James Wettenhall
• [BioC] Makefile for installing all available packages   Warnes, Gregory R
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Floor Stam
• [BioC] AFFY PLIER ALGORITHM   Anthony Bosco
• [BioC] Problem installing Rgraphviz   Kasper Daniel Hansen
• [BioC] Makefile for installing all available packages   Kasper Daniel Hansen
• [BioC] Problem installing Rgraphviz   Jeff Gentry
• [BioC] Problem installing Rgraphviz   Kasper Daniel Hansen
• [BioC] Two rma questions   Simon Kidd
• [BioC] repositories2   Christopher Albert
• [BioC] problems with Greg's installer script   Kimpel, Mark W
• [BioC] problems with Greg's installer script   Liaw, Andy
• [BioC] repositories2   Jeff Gentry
• [BioC] repositories2   Christopher Albert
• [BioC] repositories2   Jeff Gentry
• [BioC] Release 1.4 information   Jeff Gentry
• [BioC] Problem with affy   Kaushik, Narendra K
• [BioC] Question about Microarray before/after treatment, Paired Analysis   Haiyan Wu
• [BioC] Genbank to Unigene IDs   Gordon Smyth
• [BioC] Genbank to Unigene IDs partial help!   Anthony Bosco
• [BioC] Two rma questions   James MacDonald
• [BioC] General question about distribution spot   Phguardiol at aol.com
• [BioC] Genbank to Unigene IDs   A.J. Rossini
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Two rma questions   Simon Kidd
• [BioC] Genbank to Unigene IDs   James MacDonald
• [BioC] Two rma questions   James MacDonald
• [BioC] Reading SMD datasets   Jean Yee Hwa Yang
• [BioC] limma - dupcor.series   Helen Cattan
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Problem with affy   Rafael A. Irizarry
• [BioC] Re: Bioconductor Digest, Vol 14, Issue 24   Mayte Suarez-Farinas
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Marc Salit
• [BioC] Genbank to Unigene IDs   A.J. Rossini
• [BioC] limma - dupcor.series   Gordon Smyth
• [BioC] Genbank to Unigene IDs   James MacDonald
• [BioC] Genbank to Unigene IDs   John Zhang
• [BioC] Genbank to Unigene IDs   John Zhang
• [BioC] Genbank to Unigene IDs   John Zhang
• [BioC] Input of Spot output directly into marrayInput   Richard Friedman
• [BioC] Input of Spot output directly into marrayInput   Jean Yee Hwa Yang
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Genbank to Unigene IDs   Gordon Smyth
• [BioC] Multiple fields in Imagene data files   Gordon Smyth
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Two rma questions   Naomi Altman
• [BioC] limma - dupcor.series   Helen Cattan
• [BioC] limma - background correct method=none   Helen Cattan
• [BioC] limma - background correct method=none   Gordon Smyth
• [BioC] limma - dupcor.series   Gordon Smyth
• [BioC] justRMA/justGCRMA   James MacDonald
• [BioC] limma - background correct method=none   Helen Cattan
• [BioC] limma - background correct method=none   Matthew Hannah
• [BioC] limma - background correct method=none   Helen Cattan
• [BioC] Multiple fields in Imagene data files   Natalie P. Thorne
• [BioC] programming problem: running many ANOVAs   Arne.Muller at aventis.com
• [BioC] limma and paired data   Danielle Fletcher
• [BioC] Multiple fields in Imagene data files   Dick Beyer
• [BioC] programming problem: running many ANOVAs   Francois Collin
• [BioC] Genbank to Unigene IDs   Robert Gentleman
• [BioC] Newly available Affy data set   Eric
• [BioC] Genbank to Unigene IDs   Dave Waddell
• [BioC] Genbank to Unigene IDs   Barry Zeeberg
• [BioC] Affymetrix Tag3   Julia Reid
• [BioC] limma and paired data   Gordon Smyth
• [BioC] rae230b metadata   Caroline Johnston
• [BioC] [JOB] Computational Statistician   Warnes, Gregory R
• [BioC] [JOB] Toxicogenomics Statistician   Warnes, Gregory R
• [BioC] Affymetrix Tag3   Rafael A. Irizarry
• [BioC] Help   Swetha Nandyala
• [BioC] limma - arrays with different GAL files   Helen Cattan
• [BioC] CDF environment for U133_X3P   Holger Schwender
• [BioC] CDF environment for U133_X3P   James MacDonald
• [BioC] CDF environment for U133_X3P   Wolfgang Huber
• [BioC] problem with RdbiPgsql and R   javier garcia - CEBAS
• [BioC] subtractmm problem in "affy"   PARK,CHRISTOPHER CHANGSUN
• [BioC] subtractmm problem in "affy"   Ben Bolstad
• [BioC] Published studies assessing process variability   Francois Collin
• [BioC] tutorial available? [forwarded message]   Martin Maechler
• [BioC] tutorial available? [forwarded message]   Robert Gentleman
• [BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Marc Salit
• [BioC] subtractmm problem in "affy"   Anja von Heydebreck
• [BioC] just.gcrma and gcrma   Oosting, J. (PATH)
• [BioC] problem with RdbiPgsql and R   John Zhang
• [BioC] problem with RdbiPgsql and R   javier garcia - CEBAS
• [BioC] subtractmm problem in "affy"   Ben Bolstad
• [BioC] just.gcrma and gcrma   James MacDonald
• [BioC] when to call pmcorrect in affy   Arne.Muller at aventis.com
• [BioC] when to call pmcorrect in affy   Ben Bolstad
• [BioC] GO annotation problem   Mayte Suarez-Farinas
• [BioC] Follow-up: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9   Marc Salit
• [BioC] GO annotation problem   John Zhang
• [BioC] limma - arrays with different GAL files   Chris Wilkinson
• [BioC] combine part of U133A and U95Av2 affy chip   Rudy.vanEijsden at GEN.unimaas.nl
• [BioC] Genbank to Unigene IDs   Kane, David
• [BioC] Affy Bioconductor with Rat230_2 chips   Kim Gernert
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Re: Bioconductor Digest, Vol 14, Issue 37   BCM HUMAN RESOURCES
• [BioC] getting MAS for a large affy object   Hao Liu
• [BioC] Re: Bioconductor Digest, Vol 14, Issue 38   BCM HUMAN RESOURCES
• [BioC] getting MAS for a large affy object   James MacDonald
• [BioC] Affy Bioconductor with Rat230_2 chips   Crispin Miller
• [BioC] Re: Bioconductor Digest, Vol 14, Issue 39   BCM HUMAN RESOURCES
• [BioC] Dealing with artifacts on Affy chips.   Gareth Hughes
• [BioC] SAM and siggenes packages   perin
• [BioC] SAM and siggenes packages   James MacDonald
• [BioC] spotTypes function not available in limma?   V.C.L. de Jager
• [BioC] rae230bprobe library?   Andrew Harrison
• [BioC] SAM and siggenes packages   perin
• [BioC] limma publications   Julia Engelmann
• [BioC] SAM and siggenes packages   perin
• [BioC] hierarchical clustering of chips   Arne.Muller at aventis.com
• [BioC] spotTypes function not available in limma?   James Wettenhall
• [BioC] spotTypes function not available in limma?   James Wettenhall
• [BioC] Question on afy/gcrma probe indexes   Rich Haney
• [BioC] venn diagram in R   Anthony Bosco
• [BioC] venn diagram in R   Arne.Muller at aventis.com
• [BioC] SAM and siggenes packages   perin
• [BioC] venn diagram in R   Aedin
• [BioC] venn diagram in R   marcus
• [BioC] venn diagram   Anthony Bosco
• FW: [BioC] venn diagram in R   marcus
• [BioC] venn diagram   Arne.Muller at aventis.com
• [BioC] GO & KEGG   Jason Skelton
• [BioC] Question on afy/gcrma probe indexes   Wolfgang Huber
• [BioC] SAM and siggenes packages   perin
• [BioC] GO & KEGG   Sean Davis
• [BioC] GO & KEGG   John Zhang
• [BioC] Bug in affy library   Francesco Falciano
• [BioC] venn diagram   Aedin
• [BioC] RE: venn diagram   Patrick Cahan
• [BioC] RE: venn diagram   Arne.Muller at aventis.com
• [BioC] A single linear model for all   Arne.Muller at aventis.com
• [BioC] how deal with multiplicate affy probes?   Johnnidis, Jonathan
• [BioC] Question on afy/gcrma probe indexes   Park, Richard
• [BioC] how deal with multiplicate affy probes?   Robert Gentleman
• [BioC] Irizarry's paper on Stochastic Models - R-codes   Stephen Nyangoma
• [BioC] Question on afy/gcrma probe indexes   Wolfgang Huber
• [BioC] Problems with loading Rgraphviz library   yuzhen ye
• [BioC] venn diagram   Gordon Smyth
• [BioC] Question on afy/gcrma probe indexes   Rich Haney
• [BioC] Design/contrast matrix for limma   Anthony Bosco
• [BioC] Gene Logic dilution series, hgua95 identical values   Martin Jakt
• [BioC] Installation of package affy failed   Armin Schmitt
• [BioC] Difficulty in getting a boxplot display of nomralized data using affy   Ben Bolstad
• [BioC] gcrma 1.0.0 vs 1.0.6   Dick Beyer
• [BioC] Problems with loading Rgraphviz library   Jeff Gentry
• [BioC] HOMEDRIVE in R and maImage() troubles   Tarca Adi Laurentiu
• [BioC] HOMEDRIVE in R and maImage() troubles   Jeff Gentry
• [BioC] HOMEDRIVE in R and maImage() troubles   Liaw, Andy
• [BioC] Difficulty in getting a boxplot display of nomralized data using affy   Richard Friedman
• [BioC] Difficulty in getting a boxplot display of nomralized datausing affy   James MacDonald
• [BioC] RE: Design/contrast matrix for limma   Chris Wilkinson
• [BioC] Difficulty in getting a boxplot display of nomralized data using affy   Julia Engelmann
• [BioC] read.celfile   Ben Bolstad
• [BioC] algorithms and explanations   Spencer Spratt
• [BioC] Re: Classification question(Tom R. Fahland)   Tarca Adi Laurentiu
• [BioC] package hgu95av2cdf for R 1.9.0   Stephen Nyangoma
• [BioC] package hgu95av2cdf for R 1.9.0   James MacDonald
• [BioC] read.celfile   Eric Seboun
• [BioC] Re: Classification question(Tom R. Fahland)   Stephen Henderson
• [BioC] RE: Design/contrast matrix for limma   Jordi Altirriba Gutiérrez
• [BioC] Normalization of Intensities   E Motakis, Mathematics

Last message date: Fri Apr 30 22:07:27 CEST 2004
Archived on: Fri Apr 30 22:07:31 CEST 2004

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