October 2005 Archives by thread

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Starting: Sat Oct 1 08:55:47 CEST 2005
Ending: Mon Oct 31 18:56:42 CEST 2005
Messages: 292

• [BioC] Dealing with technical replication with a common reference design   Gordon Smyth
• [BioC] limma layout query (genepix GAL file)   Gordon Smyth
• [BioC] unable to compute MAD in aCGH package   Sze_Sing_LEE/DMO/NCC at nccs.com.sg
• [BioC] Venn's diagram including size   Ido M. Tamir
• [BioC] AnnBuilder URL error.   Johan Lindberg
  • [BioC] AnnBuilder URL error.   Ting-Yuan Liu
    • [BioC] AnnBuilder URL error.   Johan Lindberg
      • [BioC] AnnBuilder URL error.   Ting-Yuan Liu
• [BioC] Differential expression with bioconductor project   fede at dssm.unipa.it
  • [BioC] Differential expression with bioconductor project   Seth Falcon
• [BioC] problem with get.genes.by.pathway   Kimpel, Mark William
• [BioC] Ways to verify identity samples   =?big5?B?qLlAeXp1?=
  • [BioC] Ways to verify identity samples   James W. MacDonald
• [BioC] Barley1 annotation package?   Ann Hess
  • [BioC] Barley1 annotation package?   Ting-Yuan Liu
• [BioC] Fwd: Re: AnnBuilder-1.5.31 question   Ting-Yuan Liu
• [BioC] AnnBuilder URL error.   Ting-Yuan Liu
• [BioC] a problem with Metadat package: hgu133a2   Shi, Tao
  • [BioC] a problem with Metadat package: hgu133a2   Ting-Yuan Liu
    • [BioC] a problem with Metadat package: hgu133a2   Shi, Tao
• [BioC] coerce biomaRt martTable into data frame   Georg Otto
  • [BioC] coerce biomaRt martTable into data frame   Wolfgang Huber
• [BioC] a problem with Metadat package: hgu133a2   John Zhang
  • [BioC] a problem with Metadat package: hgu133a2   Shi, Tao
    • [BioC] a problem with Metadat package: hgu133a2   Ting-Yuan Liu
• [BioC] What is reportable?   Carolyn Fitzsimmons
• [BioC] [limma] Factorial refernce design   Ron Ophir
• [BioC] [OT] Biostatistician position available   Diego Díez Ruiz
• [BioC] [limma] Factorial refernce design   Gordon K Smyth
• [BioC] [limma] Factorial refernce design   Ron Ophir
• [BioC] (no subject)   Francesca Buffa
  • [BioC] (no subject)   Ting-Yuan Liu
• [BioC] [limma] Factorial refernce design   Gordon K Smyth
• [BioC] problem with NA   Alberto Goldoni
  • [BioC] problem with NA   Saroj Mohapatra
• [BioC] Differentially expressed gene list   carotenuto at igb.cnr.it
• [BioC] Q: phantom probsets created by combineAffyBatch?   C. Charles Gu
• [BioC] [Off Topic] Affymetrix job announcement   Cawley, Simon
• [BioC] A2R for Windows or alternative to cutree.order for windows OS   Barry Henderson
• [BioC] memory problems on IRIX machine   drnevich at uiuc.edu
• [BioC] Filtering affymetrix data   Teresa Casals
  • [BioC] Filtering affymetrix data   Robert Gentleman
• [BioC] String manipulation: String to Command   Mohammad Esad-Djou
  • [BioC] String manipulation: String to Command   Ido M. Tamir
  • [BioC] String manipulation: String to Command   Robert Gentleman
    • [BioC] goHyperG generates GO links at arrays.ucsf.edu with wrong perl script,   Saurin Jani
      • [BioC] goHyperG generates GO links at arrays.ucsf.edu with wrong perl script,   Robert Gentleman
      • [BioC] goHyperG generates GO links at arrays.ucsf.edu with wrong perl script,   Saurin Jani
      • [BioC] goHyperG generates GO links at arrays.ucsf.edu with wrong perl script,   Robert Gentleman
• [BioC] GOstat question.   Johan Lindberg
• [BioC] Job: Cancer Research UK   Gavin Kelly
• [BioC] Tcl/tk command - checkbutton problem   Sebastian Różewicz
  • [BioC] Tcl/tk command - checkbutton problem   Keith Satterley
• [BioC] Differentially expressed gene list   James MacDonald
• [BioC] Error while installing genefilter package   Nayeem Quayum
  • [BioC] Error while installing genefilter package   Francois Pepin
  • [BioC] Error while installing genefilter package   Robert Gentleman
• [BioC] AnnBuilder downloadSourceData()   Denise Mauldin
  • [BioC] AnnBuilder downloadSourceData()   Ting-Yuan Liu
    • [BioC] AnnBuilder downloadSourceData()   Denise Mauldin
• [BioC] how to generate dataset for multtest?   Assa Yeroslaviz
• [BioC] how to generate dataset for multtest?   Assa Yeroslaviz
• [BioC] Parser of Simple Omnibus Format in Text   Michal Kolar
  • [BioC] Parser of Simple Omnibus Format in Text   Sean Davis
• [BioC] Most specific common ancestor for GO terms   Lourdes Peña Castillo
• [BioC] post hoc adjustment for dye bias   Kathryn V. Steiger
• [BioC] preprocessing separately from each other   Mohammad Esad-Djou
• [BioC] MALDI-TOF data preprocessing   Marion Cortet
  • [BioC] MALDI-TOF data preprocessing   Kevin Coombes
• [BioC] delay for the new release of BioConductor ?   Benjamin Haibe-Kains
  • [BioC] delay for the new release of BioConductor ?   Seth Falcon
• [BioC] QPCR analysis (Real time)   Matjaž Hren
  • [BioC] QPCR analysis (Real time)   Markus Ruschhaupt
• [BioC] System configaration -Bioconductor for the best possible results (in terms of files processed)   Chaitanya Kommidi
• [BioC] UPDATE: a problem with Metadat package: hgu133a2 ----- Fwd: RE: Should BE964473 be mapped to Hs. 333958 or Hs. 282260?   Shi, Tao
• [BioC] problems normalizing in limma   Anand C.Patel
• [BioC] annotations for Codelink arrays   Shi, Tao
  • [BioC] annotations for Codelink arrays   Robert Gentleman
    • [BioC] annotations for Codelink arrays   Diego Díez Ruiz
• [BioC] problems normalizing in limma   Gordon Smyth
• [BioC] Source Code of affy package   BURCIN BEKTAS
  • [BioC] Source Code of affy package   Sean Davis
  • [BioC] Source Code of affy package   Ido M. Tamir
• [BioC] how to select on Present calls in 2 out of 5 chips   Andreas Zankl
  • [BioC] how to select on Present calls in 2 out of 5 chips   James W. MacDonald
• [BioC] Source Code of affy package   Sean Davis
• [BioC] how to select on Present calls in 2 out of 5 chips   Crispin Miller
• [BioC] how to select on Present calls in 2 out of 5 chips   Claire Wilson
• [BioC] problems normalizing in limma   Anand C. Patel
• [BioC] gpr.gz   Rafael A. Irizarry
  • [BioC] gpr.gz   Sean Davis
  • [BioC] gpr.gz   Robert Gentleman
    • [BioC] gpr.gz   Rafael A. Irizarry
      • [BioC] gpr.gz   Henrik Bengtsson
• [BioC] gpr.gz   Sean Davis
• [BioC] PLIER affinities   Jeremy Gollub
  • [BioC] PLIER affinities   James W. MacDonald
• [BioC] annotations for Codelink arrays   John Zhang
  • [BioC] annotations for Codelink arrays   Diego Diez Ruiz
• [BioC] How to get P/A/M calls using pmonly or sbutractmm   Nayeem Quayum
  • [BioC] How to get P/A/M calls using pmonly or sbutractmm   James W. MacDonald
• [BioC] How to plot just "Present" genes?   Yoder, Sean J.
  • [BioC] How to plot just "Present" genes?   James W. MacDonald
• [BioC] siggenes error with rma & wilcoxon test   Ken Termiso
  • [BioC] siggenes error with rma & wilcoxon test   Holger Schwender
• [BioC] Limma read GenePix version 6 file   Ye, Bin
  • [BioC] Limma read GenePix version 6 file   Saroj Mohapatra
• [BioC] Limma read GenePix version 6 file   Ye, Bin
• [BioC] goHyperG generates GO links at arrays.ucsf.edu withwrong perl script,   Paquet, Agnes
• [BioC] ANN: Bioconductor Release 1.7 is available   Seth Falcon
  • [BioC] Release 1.7 - Oligo package?   Mikko Arvas
    • [BioC] Release 1.7 - Oligo package?   Seth Falcon
    • [BioC] Release 1.7 - Oligo package?   Benilton Carvalho
  • [BioC] ANN: Bioconductor Release 1.7 is available   Wolfgang Huber
• [BioC] Limma read GenePix version 6 file   Gordon Smyth
• [BioC] bg.adjust.gcrma   zhxiaoyu at ucla.edu
  • [BioC] bg.adjust.gcrma   James W. MacDonald
• [BioC] calculation of "M" in limma topTable   Kimpel, Mark William
  • [BioC] calculation of "M" in limma topTable   James W. MacDonald
• [BioC] ANN: Bioconductor Release 1.7 is available   Norman Pavelka
  • [BioC] ANN: Bioconductor Release 1.7 is available   stefano iacus
    • [BioC] ANN: Bioconductor Release 1.7 is available   Norman Pavelka
• [BioC] Affy Exon Array Analysis   Dr. Reinhard Hoffmann
• [BioC] affylmGUI error   Pedro Botías
• [BioC] annotations for Codelink arrays   John Zhang
• [BioC] limma(B) and maanova(La.svd) questions   Aurélie Laugraud
• [BioC] Cannot find xml2-config   Marcelo Luiz de Laia
  • [BioC] Cannot find xml2-config   Seth Falcon
• [BioC] Opinion on proceeding strategy   Marco Gentilini
• [BioC] medpolish Warning   Nayeem Quayum
  • [BioC] medpolish Warning   James W. MacDonald
• [BioC] Documentation of bioDist and geneSOM   Nayeem Quayum
  • [BioC] Documentation of bioDist and geneSOM   Kasper Daniel Hansen
    • [BioC] Documentation of bioDist and geneSOM   Robert Gentleman
• [BioC] problem normalizeMedians (limma)   Francois Pepin
• [BioC] Limma read GenePix version 6 file   Gordon Smyth
• [BioC] [OT] Help to creating a function to automate the plotProfile function in timecourse   Marcelo Luiz de Laia
  • [BioC] [OT] Help to creating a function to automate the plotProfile function in timecourse   Ido M. Tamir
• [BioC] book   Robert Gentleman
• [BioC] PLIER affinities redux   Jeremy Gollub
  • [BioC] PLIER affinities redux   James W. MacDonald
    • [BioC] PLIER affinities redux   Jeremy Gollub
      • [BioC] PLIER affinities redux   James W. MacDonald
• [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLM procedures   Groot, Philip de
• [BioC] Affymetrix gtype_cel_to_pq   Henrik Bengtsson
  • [BioC] Affymetrix gtype_cel_to_pq   Cawley, Simon
  • [BioC] Affymetrix gtype_cel_to_pq   Kasper Daniel Hansen
  • [BioC] Affymetrix gtype_cel_to_pq   Kasper Daniel Hansen
• [BioC] help with transpose   Alberto Goldoni
  • [BioC] help with transpose   Sean Davis
• [BioC] help on proceeding strategy   Marco Gentilini
• [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures   Groot, Philip de
  • [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures   Ben Bolstad
• [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures   Groot, Philip de
  • [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures   Ben Bolstad
• [BioC] package xtable   Li,Qinghong,ST.LOUIS,Molecular Biology
  • [BioC] package xtable   Seth Falcon
• [BioC] PLIER affinities redux   Matthew Hannah
  • [BioC] PLIER affinities redux   Jeremy Gollub
• [BioC] error in getMonograph() - many packages not available   Jenny Drnevich
  • [BioC] error in getMonograph() - many packages not available   Seth Falcon
• [BioC] effect of normalization on class prediction?   Jenny Drnevich
• [BioC] problem normalizeMedians (limma)   Gordon Smyth
  • [BioC] problem normalizeMedians (limma)   Marcus Davy
    • [BioC] problem normalizeMedians (limma)   Gordon Smyth
• [BioC] PLIER affinities redux   Crispin Miller
• [BioC] Limma time course analysis : determining positively and negatively reg genes   Ken Termiso
  • [BioC] Limma time course analysis : determining positively and negatively reg genes   Sean Davis
• [BioC] ANCOVA in limma   Naomi Altman
• [BioC] hexbin in R 2.2.0 - installation problem   Naomi Altman
  • [BioC] hexbin in R 2.2.0 - installation problem   Marcus Davy
  • [BioC] hexbin in R 2.2.0 - installation problem   Seth Falcon
    • [BioC] hexbin in R 2.2.0 - installation problem   Naomi Altman
  • [BioC] hexbin in R 2.2.0 - installation problem   Ido M. Tamir
• [BioC] Upcoming system maintenance - Oct 24, 14:00PST   Seth Falcon
• [BioC] GO2PROBES   Simon Lin
  • [BioC] GO2PROBES   Robert Gentleman
• [BioC] biocLite script and R 2.3   Wolfgang Huber
  • [BioC] biocLite script and R 2.3   Seth Falcon
  • [BioC] biocLite script and R 2.3   Seth Falcon
• [BioC] AnnBuilder results question.   Johan Lindberg
  • [BioC] AnnBuilder results question.   Robert Gentleman
• [BioC] R-2.2.0 + R.app 1.13   stefano iacus
• [BioC] package search   Alberto Goldoni
  • [BioC] package search   Sean Davis
• [BioC] configuraing goCluster   madhurima bhattacharjee
  • [BioC] configuraing goCluster   Gunnar Wrobel
  • [BioC] configuraing goCluster   Seth Falcon
• [BioC] Affy Exon Array Analysis   Justin Borevitz
• [BioC] limma(B) and maanova(La.svd) questions   Aurélie Laugraud
• [BioC] help for SOM package   Nayeem Quayum
• [BioC] Affy Exon Array Analysis   Justin Borevitz
• [BioC] GO package   Khan, Sohail
  • [BioC] GO package   Seth Falcon
  • [BioC] GO package   James W. MacDonald
  • [BioC] GO package   Beatriz
    • [BioC] GO package   Seth Falcon
• [BioC] ANCOVA in limma   Gordon Smyth
• [BioC] hexbin in R 2.2.0 - installation problem   Nicholas Lewin-Koh
• [BioC] please recommend   Weiwei Shi
  • [BioC] please recommend   Naomi Altman
• [BioC] please recommend   James MacDonald
• [BioC] help regardig som package to do clustering   Nayeem Quayum
• [BioC] R Programmer/Analyst   Earl F. Glynn
• [BioC] Redirected to BioC Re: [Bioc-devel] aafTableAnn() in annaffy_1.0.18 ?   James W. MacDonald
• [BioC] sum.sam.out   Assa Yeroslaviz
  • [BioC] sum.sam.out   Nicolas Servant
• [BioC] installation warnings and other related questions   Weiwei Shi
  • [BioC] installation warnings and other related questions   Seth Falcon
    • [BioC] installation warnings and other related questions   Seth Falcon
      • [BioC] installation warnings and other related questions   Weiwei Shi
      • [BioC] installation warnings and other related questions   lgautier at altern.org
• [BioC] IRC channel?   Steve Lee
  • [BioC] IRC channel?   Seth Falcon
    • [BioC] IRC channel?   Dirk Eddelbuettel
• [BioC] Setting exprSet values   Daniel Pick
  • [BioC] Setting exprSet values   Wolfgang Huber
• [BioC] Cannot load bioconductor's packages installed   =?gb2312?B?1qPkvw==?=
  • [BioC] Cannot load bioconductor's packages installed   Li Long
  • [BioC] Cannot load bioconductor's packages installed   Seth Falcon
• [BioC] Limma: ordinary t-test is based on equal variances?   Groot, Philip de
• [BioC] Glyco gene chip   Binita Dutta
  • [BioC] Glyco gene chip   James W. MacDonald
    • [BioC] Glyco gene chip   M Perez
• [BioC] error about using dnacopy package   yingk
• [BioC] Help with searching GO in R   Christina Demos
• [BioC] Help with searching GO in R   John Zhang
• [BioC] list problem   Andreas Zankl
• [BioC] list problem   John Zhang
  • [BioC] list problem   Andreas Zankl
    • [BioC] list problem   James W. MacDonald
• [BioC] limma and 'randomizedBlockFit' is deprecate   Naomi Altman
• [BioC] passing my data to siggenes package   madhurima bhattacharjee
  • [BioC] passing my data to siggenes package   Sean Davis
• [BioC] passing my data to siggenes package   Sean Davis
  • [BioC] passing my data to siggenes package   Holger Schwender
• [BioC] Affymetrix question   lucia García
  • [BioC] Affymetrix question   James W. MacDonald
    • [BioC] Affymetrix question   Jenny Drnevich
• [BioC] Celegans data package?   Wolfgang Huber
• [BioC] heatmap-suppress col reordering/dendrogram?   Ann Hess
  • [BioC] heatmap-suppress col reordering/dendrogram?   Sean Davis
• [BioC] How to retrieve the intensity of probes (PM and MM) and the order of probes in the probe set?   szhan at uoguelph.ca
• [BioC] heatmap-suppress col reordering/dendrogram?   Sean Davis
• [BioC] bioconductor 1.7 and kooperberg   scholz at Ag.arizona.edu
• [BioC] background correction with cDNA array data   Qi.Zhang at astrazeneca.com
  • [BioC] background correction with cDNA array data   Naomi Altman
  • [BioC] background correction with cDNA array data   Giuseppe.Palermo at bo.infn.it
• [BioC] limma and 'randomizedBlockFit' is deprecate   Gordon K Smyth
• [BioC] background correction with cDNA array data   Qi.Zhang at astrazeneca.com
  • [BioC] background correction with cDNA array data   David Ruau
• [BioC] background correction with cDNA array data   Sean Davis
• [BioC] bioconductor 1.7 and kooperberg   Gordon K Smyth
• [BioC] Rgraphviz load problem   Fridlyand, Jane
  • [BioC] Rgraphviz load problem   Byron Ellis
    • [BioC] Rgraphviz load problem   Kasper Daniel Hansen
    • [BioC] Rgraphviz load problem   Fridlyand, Jane
    • [BioC] Rgraphviz load problem   Seth Falcon
      • [BioC] Rgraphviz load problem   Byron Ellis
      • [BioC] Rgraphviz load problem   Seth Falcon
• [BioC] Rgraphviz load problem   Jeff Gentry
• [BioC] Rgraphviz load problem   Jane Fridlyand
  • [BioC] Rgraphviz load problem : 2nd question for MAC OS users   Jane Fridlyand
    • [BioC] Rgraphviz load problem : 2nd question for MAC OS users   Sean Davis
    • [BioC] Rgraphviz load problem : 2nd question for MAC OS users   Todd Richmond
    • [BioC] Rgraphviz load problem : 2nd question for MAC OS users   Seth Falcon
  • [BioC] Rgraphviz load problem   Rob J Goedman
• [BioC] makepackage of affy's 100K and 500K SNP chip   Zhang, Jacob
  • [BioC] makepackage of affy's 100K and 500K SNP chip   Rafael A. Irizarry
  • [BioC] makepackage of affy's 100K and 500K SNP chip   Benilton Carvalho
  • [BioC] calibrating an exprSet on a specific probeset   Celine Carret
• [BioC] replace error reading 2color txt data into limma   Susan J. Miller
• [BioC] heatmap-suppress col reordering/dendrogram?   Lourdes Peña Castillo
• [BioC] is Biostrings being maintained?   Marcus G. Daniels
  • [BioC] is Biostrings being maintained?   Robert Gentleman
    • [BioC] is Biostrings being maintained?   Antoine Lucas
• [BioC] siggenes package   madhurima bhattacharjee
  • [BioC] siggenes package   Holger Schwender
• [BioC] calculation of s0 (siggenes)   Assa Yeroslaviz
  • [BioC] calculation of s0 (siggenes)   Holger Schwender
• [BioC] list of significant genes (siggenes)   Assa Yeroslaviz
  • [BioC] list of significant genes (siggenes)   Seth Falcon
• [BioC] list of significant genes (siggenes)   Holger Schwender
• [BioC] Using limma with Applied Precision SoftWorx data   Susan J. Miller
• [BioC] New version of prada available in 1.7 release   Seth Falcon
• [BioC] problems with biomaRt on Mac OS X (10.4.2 = Tiger)   Jane Fridlyand
• [BioC] getting end position of genes   Andreas Zankl
  • [BioC] getting end position of genes   Sean Davis
• [BioC] IRC channel   Steve Lee
• [BioC] replace error reading 2color txt data into limma   Gordon Smyth
• [BioC] Bioconductor on CD-ROM   jro203
• [BioC] getting end position of genes   John Zhang

Last message date: Mon Oct 31 18:56:42 CEST 2005
Archived on: Thu Nov 3 02:06:24 CEST 2005

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