September 2004 Archives by subject

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Starting: Wed Sep 1 02:33:26 CEST 2004
Ending: Thu Sep 30 19:54:11 CEST 2004
Messages: 296

• [BioC] (no subject)   Paul Boutros
• [BioC] [Fwd: Re: using gcrma in expresso]   echang4 at life.uiuc.edu
• [BioC] A question about MAS5 vs RMA vs GCRMA   YUK FAI LEUNG
• [BioC] A question about MAS5 vs RMA vs GCRMA   Adaikalavan Ramasamy
• [BioC] A question about MAS5 vs RMA vs GCRMA   Martino Barenco
• [BioC] A question about MAS5 vs RMA vs GCRMA   YUK FAI LEUNG
• [BioC] about siggenes   haojie
• [BioC] about siggenes   Robert Gentleman
• [BioC] about siggenes   Holger Schwender
• [BioC] about siggenes   haojie
• [BioC] Advice on print-tip normalization   Gene Cutler
• [BioC] affy and limma   Gareth Elvidge
• [BioC] Affy empty line   Hee Siew Wan
• [BioC] Affymetrix is changing its labelling kit - data analysiswill change!?   Francois Collin
• [BioC] Affymetrix is changing its labelling kit - data analysis will change!?   Matthew Hannah
• [BioC] Affymetrix P calls   Stephen Henderson
• [BioC] Affymetrix P calls   Susmita Datta
• [BioC] AnnBuilder   Catalin Barbacioru
• [BioC] AnnBuilder   Robert Gentleman
• [BioC] AnnBuilder/ABPkgBuilder: lots of Errors   Floor Stam
• [BioC] AnnBuilder/ABPkgBuilder: lots of Errors   John Zhang
• [BioC] AnnBuilder/ABPkgBuilder: lots of Errors   Floor Stam
• [BioC] AnnBuilder/ABPkgBuilder: lots of Errors   John Zhang
• [BioC] Application of PAMR from Affy to spot data   Tan, MinHan
• [BioC] Application of PAMR from Affy to spot data   Robert Gentleman
• [BioC] averaging expression values in limma   Ana Conesa
• [BioC] Bad Data Sets needed!   michael watson (IAH-C)
• [BioC] Bioconductor release 1.5 notes   Jeff Gentry
• [BioC] bug in reposTools 1.4.11: missing getRversion   Jeff Gentry
• [BioC] bug in reposTools 1.4.11: missing getRversion   Ivo Kwee
• [BioC] Calculating microarray ratios between channels from different arrays   michael watson (IAH-C)
• [BioC] Common reference design and intercept in limma   Sean Davis
• [BioC] Common reference design and intercept in limma   Gordon K Smyth
• [BioC] contrasts.fit Error   Matt McCall
• [BioC] contrasts.fit Error   Gordon K Smyth
• [BioC] contrasts.fit Error   Matt McCall
• [BioC] contrasts.fit Error   Gordon K Smyth
• [BioC] Correct use of a distance measure when clustering gene expression data   michael watson (IAH-C)
• [BioC] Correct use of a distance measure when clustering gene expression data   Floor Stam
• [BioC] Creating a substet of probe intensities from AffyBatch object   Larry.Lapointe at csiro.au
• [BioC] Creating a substet of probe intensities from AffyBatch object   Laurent Gautier
• [BioC] Creating a substet of probe intensities from AffyBatch object   Larry La Pointe
• [BioC] dChip   Lizhe Xu
• [BioC] dChip   Ben Bolstad
• [BioC] Do I now understand Limma contrast matrices??   Matthew Hannah
• [BioC] Error getting packages from repository   Sean Davis
• [BioC] Error getting packages from repository   Jeff Gentry
• [BioC] Error getting packages from repository   Sean Davis
• [BioC] Error in kooperberg procedure   michael watson (IAH-C)
• [BioC] Error in kooperberg procedure   Matthew Ritchie
• [BioC] Error with library(limma) with R2.0 devel   Matthew Hannah
• [BioC] Error with library(limma) with R2.0 devel   Gordon Smyth
• [BioC] Error with library(limma) with R2.0 devel   Jeff Gentry
• [BioC] Error with library(limma) with R2.0 devel   Matthew Hannah
• [BioC] Error with library(limma) with R2.0 devel   James W. MacDonald
• [BioC] error with update.package2   Adaikalavan Ramasamy
• [BioC] error with update.package2   Adaikalavan Ramasamy
• [BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel   Matthew Hannah
• [BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel   Matthew Hannah
• [BioC] Errors with -Inf   michael watson (IAH-C)
• [BioC] excluding absent genes - again   Arne.Muller at aventis.com
• [BioC] Expression levels in GCRMA and MAS5.0 and cut-off   Jordi Altirriba Gutiérrez
• [BioC] Expression levels in GCRMA and MAS5.0 and cut-off   Zhijin Wu
• [BioC] Expression levels in GCRMA and MAS5.0 and cut-off   Jordi Altirriba Gutiérrez
• [BioC] Extracting normalized intensities   Gene Cutler
• [BioC] Extracting normalized intensities   Jean Yee Hwa Yang
• [BioC] fibroblasts and endothelial cells   Ulrich Pfeffer
• [BioC] fibroblasts and endothelial cells   Phguardiol at aol.com
• [BioC] Finding and controlling for dye bias in Limma   Sean Davis
• [BioC] Finding and controlling for dye bias in Limma   Gordon K Smyth
• [BioC] Friedman test   Arne.Muller at aventis.com
• [BioC] function pubmed and large requests   Kimpel, Mark W
• [BioC] gcrma background   Ariel Chernomoretz
• [BioC] gcrma background   Zhijin Wu
• [BioC] GCRMA publication   Margaret Gardiner-Garden
• [BioC] GCRMA publication   Steffen Durinck
• [BioC] GCRMA publication   Zhijin Wu
• [BioC] GCRMA/RMA bimodal distribution   Matthew Hannah
• [BioC] HGU95A and HGU95ACDF   S Peri
• [BioC] HGU95A and HGU95ACDF   John Zhang
• [BioC] high poportion of identical expression measure with RMA and 3 arrays (addendum)   Adaikalavan Ramasamy
• [BioC] high poportion of identical expression measure with RMA and 3 arrays   Adaikalavan Ramasamy
• [BioC] How do I make exprSet?   Hao Liu
• [BioC] How do I make exprSet?   Robert Gentleman
• [BioC] how to do MAS background correction for Mismatch?   F Duan
• [BioC] how to do MAS background correction for Mismatch?   James W. MacDonald
• [BioC] how to do MAS background correction for Mismatch?   F Duan
• [BioC] How to get gene names in arabidopsis arrays   Fangxin Hong
• [BioC] How to get gene names in arabidopsis arrays   Robert Gentleman
• [BioC] How to save image to JPEG version under Linux?   F Duan
• [BioC] How to save image to JPEG version under Linux?   Zhijin Wu
• [BioC] How to save image to JPEG version under Linux?   Sean Davis
• [BioC] IBM developerworks article on R (intro, part 1)   Paul Grosu
• [BioC] identify gene expression markers using Bayesian   Liu, Xin
• [BioC] Install HGU133a_tag in Linux.   Lei Zhou
• [BioC] Install HGU133a_tag in Linux.   Jeff Gentry
• [BioC] Is it right?   Kaushik, Narendra K
• [BioC] Is it right?   michael watson (IAH-C)
• [BioC] Is it right?   Caimiao Wei
• [BioC] Kooperberg   Jason Skelton
• [BioC] Kooperberg   Matthew Ritchie
• [BioC] latest devel GO package not built in R2.0.0   Dick Beyer
• [BioC] latest devel GO package not built in R2.0.0   John Zhang
• [BioC] latest devel GO package not built in R2.0.0   Dick Beyer
• [BioC] latest devel GO package not built in R2.0.0   John Zhang
• [BioC] Li Wong PM-only "background" correction   Ann Hess
• [BioC] Li Wong PM-only "background" correction   Laurent Gautier
• [BioC] limma & targets   Giovanni Coppola
• [BioC] limma & targets   Gordon Smyth
• [BioC] limma Dye Swap question   Mike Schaffer
• [BioC] limma Dye Swap question   Ramon Diaz-Uriarte
• [BioC] limma moderated t-statistics and B-statistics   Gordon Smyth
• [BioC] LimmaGUI Background corrections   Elizabeth Brooke-Powell
• [BioC] Loading gal files with marray   Daniel Iordan
• [BioC] Loading gal files with marray   Daniel Iordan
• [BioC] Loess normalization for Agilent chips   Malard, Joel M
• [BioC] Loess normalization for Agilent chips   A.J. Rossini
• [BioC] Loess normalization for Agilent chips   Malard, Joel M
• [BioC] MAS problem   Michael Barnes
• [BioC] MAS problem   Adaikalavan Ramasamy
• [BioC] MAS, RMA or DChip. Which is better?   narinder.singh
• [BioC] MAS5 and GCOC difference to get CEL files   Delphine Fleury
• [BioC] MAS5 and GCOC difference to get CEL files   Adaikalavan Ramasamy
• [BioC] MAS5 and GCOC difference to get CEL files   James W. MacDonald
• [BioC] MAS5 and GCOC difference to get CEL files   Adaikalavan Ramasamy
• [BioC] MAS5 and GCOC difference to get CEL files   Remo Sanges
• [BioC] MAS5 and GCOC difference to get CEL files   Matthew Hannah
• [BioC] mas5calls error with YG_S98 CEL files   Bruz Marzolf
• [BioC] mas5calls error with YG_S98 CEL files   Bruz Marzolf
• [BioC] mas5calls error with YG_S98 CEL files   Crispin Miller
• [BioC] matchprobes for GCRMA   Victoria Perreau
• [BioC] matchprobes for GCRMA   Adaikalavan Ramasamy
• [BioC] memory management in Win XP   Kimpel, Mark W
• [BioC] memory management in Win XP   Robert Gentleman
• [BioC] Metadata for Atgenome1 array   andy phillips (RRes-Roth)
• [BioC] Metamorph   E Motakis, Mathematics
• [BioC] missing xy2i and i2xy functions   Nisha Mulakken
• [BioC] missing xy2i and i2xy functions   James MacDonald
• [BioC] Modelling interaction using limma package   Ramon Diaz-Uriarte
• [BioC] Modelling interaction using limma package   Fangxin Hong
• [BioC] Modelling interaction using limma package   Ramon Diaz-Uriarte
• [BioC] Modelling interaction using limma package   Fangxin Hong
• [BioC] Normalisation of focussed arrays and Taq-man gene cards   Aedin
• [BioC] Normalising divergent samples.   Matthew Hannah
• [BioC] Normalising divergent samples.   Arne.Muller at aventis.com
• [BioC] normalize.invariantset   cchetia at vbi.vt.edu
• [BioC] normalize.invariantset   cchetia at vbi.vt.edu
• [BioC] number of grid columns is not 4 - error   Morten
• [BioC] number of grid columns is not 4 - error   Gordon K Smyth
• [BioC] odd results from vennCounts()   Jacqueline Hall
• [BioC] odd results from vennCounts()   Gordon Smyth
• [BioC] odd results from vennCounts()   Gordon Smyth
• [BioC] Package for ArrayWoRx output-files   Kim Holmstrøm
• [BioC] package mgu74av2 version 2.0.0 install   Florence Combes
• [BioC] package mgu74av2 version 2.0.0 install   John Zhang
• [BioC] package mgu74av2 version 2.0.0 install   Florence Combes
• [BioC] package mgu74av2 version 2.0.0 install   Jeff Gentry
• [BioC] package mgu74av2 version 2.0.0 install   Florence Combes
• [BioC] package Ruuid   alberto goldoni
• [BioC] package Ruuid   Robert Gentleman
• [BioC] package Ruuid   alberto goldoni
• [BioC] package Ruuid   Douglas Bates
• [BioC] plot.ProbeSet   Peter Lee
• [BioC] Problem with BioC   Kaushik, Narendra K
• [BioC] Problem with BioC   Robert Gentleman
• [BioC] Problem with BioC   James MacDonald
• [BioC] Problem with BioC   Jeff Gentry
• [BioC] Problem with gls.series in limma   Fangxin Hong
• [BioC] Problem with gls.series in limma   Gordon Smyth
• [BioC] Problems with BioConductor   Alexandra-mariela Dumitru
• [BioC] Problems with BioConductor   Jeff Gentry
• [BioC] Question   Sandya Liyanarachchi
• [BioC] Question   alberto goldoni
• [BioC] question about distribution   Phguardiol at aol.com
• [BioC] questions about U133A cdf packages   Wenlei Liu
• [BioC] questions about U133A cdf packages   James W. MacDonald
• [BioC] r devel ????   Alberto Goldoni
• [BioC] r devel ????   James W. MacDonald
• [BioC] r devel ????   Kasper Daniel Hansen
• [BioC] r devel ????   Jeff Gentry
• [BioC] RBGL 1.2.2 compilation problem   Roels, Steven
• [BioC] Re: [R] unable to download   Jeff Gentry
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] Re: [S] Error in clustering procedure   James W. MacDonald
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] Re: [S] Error in clustering procedure   David K Pritchard
• [BioC] Re: [S] Error in clustering procedure   Ramon Diaz-Uriarte
• [BioC] Re: [S] Error in clustering procedure   Prof Brian Ripley
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] Re: [S] Error in clustering procedure   michael watson (IAH-C)
• [BioC] Re: [S] Error in clustering procedure   Prof Brian Ripley
• [BioC] Re: [S] Error in clustering procedure   michael watson (IAH-C)
• [BioC] Re: [S] Error in clustering procedure   michael watson (IAH-C)
• [BioC] Re: [S] Error in clustering procedure   Ramon Diaz-Uriarte
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] Re: [S] Error in clustering procedure   Liaw, Andy
• [BioC] Re: [S] Error in clustering procedure   Stephen Henderson
• [BioC] Re: [S] Error in clustering procedure   cstrato
• [BioC] RE: Advice on print-tip normalization   Reimers, Mark (NIH/NCI)
• [BioC] RE: Advice on print-tip normalization   Gordon K Smyth
• [BioC] RE: Advice on print-tip normalization   Ramon Diaz-Uriarte
• [BioC] Re: Advice on print-tip normalization   Gene Cutler
• [BioC] Re: Advice on print-tip normalization   Adaikalavan Ramasamy
• [BioC] RE: Advice on print-tip normalization   Gene Cutler
• [BioC] Re: Bioconductor Digest, Vol 19, Issue 26   Eric
• [BioC] RE: Errors with -Inf   michael watson (IAH-C)
• [BioC] RE: Errors with -Inf   Gordon K Smyth
• [BioC] Re: LimmaGUI Background corrections   Gordon K Smyth
• [BioC] Re: LimmaGUI Background corrections   James Wettenhall
• [BioC] Re: LimmaGui on Mac OSX (version 10.3.5)   James Wettenhall
• [BioC] RE: Normalising divergent samples.   Matthew Hannah
• [BioC] RE: RMA normalization   Reimers, Mark (NIH/NCI)
• [BioC] RE: RMA normalization   Dalphin, Mark
• [BioC] RE: RMA normalization   Matthew Hannah
• [BioC] RE: RMA normalization   w.huber at dkfz-heidelberg.de
• [BioC] Re: Unequally spaced replicates in limma - "sort your MA object by gene ID "   Saroj Mohapatra
• [BioC] Read.maimages question   michael watson (IAH-C)
• [BioC] Read.maimages question   Gordon K Smyth
• [BioC] Read.maimages question   Gordon Smyth
• [BioC] Read.maimages question   michael watson (IAH-C)
• [BioC] Reading mev files into bioC   Tarca Adi Laurentiu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Regarding Rgraphviz compilation error   Saurin Jani
• [BioC] Regarding Rgraphviz compilation error   Jeff Gentry
• [BioC] Regarding Rgraphviz compilation error   Saurin Jani
• [BioC] Regarding Rgraphviz compilation error   Jeff Gentry
• [BioC] Rgraphviz + graphviz 1.12.1 compilation error   Saurin Jani
• [BioC] Rgraphviz + graphviz 1.12.1 compilation error   Jeff Gentry
• [BioC] Rgraphviz Error : Rgraphviz.c: In function `Rgraphviz_agopen':   Saurin Jani
• [BioC] Rgraphviz install issues   Andrew Beckerman
• [BioC] Rgraphviz install issues   Jeff Gentry
• [BioC] Rgraphviz: read .dot file   Xiao-Jun Ma
• [BioC] Rgraphviz: read .dot file   Vincent Carey 525-2265
• [BioC] RMA normalization   Adaikalavan Ramasamy
• [BioC] RMA normalization   Adaikalavan Ramasamy
• [BioC] RMA normalization   Fangxin Hong
• [BioC] RMA normalization   Hairong Wei
• [BioC] RMA outline   Lawrence-Paul Petalidis
• [BioC] rma question   Hairong Wei
• [BioC] rma question   Hairong Wei
• [BioC] rma question   Adaikalavan Ramasamy
• [BioC] SAM: the fudge factor in Siggenes and Excel   Caimiao Wei
• [BioC] SE and memory problems   Florence Combes
• [BioC] SE in RMA and GCRMA   Florence Combes
• [BioC] SE in RMA and GCRMA   Davide
• [BioC] SE in RMA and GCRMA   Zhijin Wu
• [BioC] Selecting p-value cutoffs for differential expression   Matthew Hannah
• [BioC] Selecting p-value cutoffs for differential expression   Ramon Diaz-Uriarte
• [BioC] Selecting p-value cutoffs for differential expression   Suresh Gopalan
• [BioC] Selecting p-value cutoffs for differential expression   Suresh Gopalan
• [BioC] superpc - 'group' and 'Cox score'   Liu, Xin
• [BioC] superpc - 'group' and 'Cox score'   Liu, Xin
• [BioC] superpc - 'group' and 'Cox score'   James W. MacDonald
• [BioC] SV:Package for ArrayWoRx output-files   Per Gregersen
• [BioC] Swiss-Prot to gene annotation translation/conversion   Kimpel, Mark W
• [BioC] Swiss-Prot to gene annotation translation/conversion   Sean Davis
• [BioC] Terminology was RE: RMA normalization   Ben Bolstad
• [BioC] Terminology was RE: RMA normalization   w.huber at dkfz-heidelberg.de
• [BioC] Terminology was RE: RMA normalization   Laurent Gautier
• [BioC] to extract just some columns of an exprsSet   Florence Combes
• [BioC] to extract just some columns of an exprsSet   Vincent Carey 525-2265
• [BioC] Trouble Loading RBGL   Jeff Lande
• [BioC] Trouble Loading RBGL   Jeff Gentry
• [BioC] Unequally spaced replicates in limma   michael watson (IAH-C)
• [BioC] Unequally spaced replicates in limma   Gordon K Smyth
• [BioC] Unequally spaced replicates in limma   michael watson (IAH-C)
• [BioC] Unequally spaced replicates in limma   Gordon Smyth
• [BioC] Unequally spaced replicates in limma   Elizabeth Brooke-Powell
• [BioC] Unequally spaced replicates in limma - "sort your MA object by gene ID "   Jakob Hedegaard
• [BioC] Unequally spaced replicates in limma - 'sort your MA object by gene ID '   Gordon K Smyth
• [BioC] Unique probes on all human affy chips   S Peri
• [BioC] Unique probes on all human affy chips   S Peri
• [BioC] Unique probes on all human affy chips   Adaikalavan Ramasamy
• [BioC] Unique probes on all human affy chips   Robert Gentleman
• [BioC] Unique probes on all human affy chips   Laurent Gautier
• [BioC] Unique probes on all human affy chips   Laurent Gautier
• [BioC] using getPMID with non-affy data   Kimpel, Mark W
• [BioC] using getPMID with non-affy data   Robert Gentleman
• [BioC] using getPMID with non-affy data   Sean Davis
• [BioC] using mat.samp in siggenes   Kathleen Kerr
• [BioC] using mat.samp in siggenes   James W. MacDonald
• [BioC] using mat.samp in siggenes   Holger Schwender
• [BioC] using mat.samp in siggenes   Kathleen Kerr
• [BioC] using mat.samp in siggenes   Holger Schwender
• [BioC] Weight functions for Agilent chips (limma)   Malard, Joel M
• [BioC] Weight functions for Agilent chips (limma)   Giovanni Coppola
• [BioC] Weight functions for Agilent chips (limma)   Malard, Joel M
• [BioC] Weight functions for Agilent chips (limma)   Giovanni Coppola
• [BioC] which library - identify gene expression markers using Bayesian   Liu, Xin
• [Fwd: RE: [BioC] RMA normalization]   Adaikalavan Ramasamy
• Flagging spots (was: [BioC] Bioconductor documentation   Gordon Smyth
• Fw: [BioC] Affy Bioconductor with Rat230_2 chips   Ali A. Pirani
• Fwd: Re: [BioC] Problem with gls.series in limma   Gordon Smyth
• GOT IT Re: [BioC] to extract just some columns of an exprsSet   Florence Combes

Last message date: Thu Sep 30 19:54:11 CEST 2004
Archived on: Thu Sep 30 19:53:24 CEST 2004

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