December 2004 Archives by date

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Starting: Wed Dec 1 00:41:17 CEST 2004
Ending: Fri Dec 31 06:39:30 CEST 2004
Messages: 227

• [BioC] BioConductor Deployment at a large site, suggestions?   Brian K Smith
• [BioC] BioConductor Deployment at a large site, suggestions?   Jeff Gentry
• [BioC] normalisation or analysis with batch effects   Arne.Muller at aventis.com
• [BioC] Re: normalisation or analysis with batch effects   Darlene Goldstein
• [BioC] Limma and limmaGUI with Imagene files, problems/bugs report   Dr. Ir. B. van Breukelen
• [BioC] Limma and limmaGUI with Imagene files, problems/bugs report   STKH (Steen Krogsgaard)
• [BioC] Perl interface   hrishikesh deshmukh
• [BioC] BioConductor Deployment at a large site, suggestions?   Brian K Smith
• [BioC] layout for maQualityPlots   Jean Yee Hwa Yang
• [BioC] Re: normalisation or analysis with batch effects   James W. MacDonald
• [BioC] aCGH modify plotting method   Christopher, Neil (NIH/NCI)
• [BioC] Re: problem with hexbin   Yanqin Yang
• [BioC] aCGH modify plotting method   James W. MacDonald
• [BioC] problem for reading Agilent Human 44k data by marray package   Yanqin Yang
• [BioC] correcting for 3' bias in highly amplified RNA samples and Affyme trix chips   Wittner, Ben
• [BioC] tandem MS question   Xiaochun Li
• [BioC] limma single channel analysis   Na, Ren
• [BioC] tandem MS question   David Lee Duewer
• [BioC] Re: problem with hexbin   Paquet, Agnes
• [BioC] justRMA segmentation fault when calculating expr.   Ulas Karaoz
• [BioC] upgrading to BioC 1.5 under R 2.0.1   Dennis Hazelett
• [BioC] Perl interface   Sean Davis
• [BioC] Limma and limmaGUI with Imagene files, problems/bugs report   Gordon K Smyth
• [BioC] AffyRNAdeg simple question   Remo Sanges
• [BioC] RE: correcting for 3' bias in highly amplified RNA samples   Reimers, Mark (NIH/NCI)
• [BioC] AffyRNAdeg simple question   James W. MacDonald
• [BioC] kyte and doolittle hydropathy values/plot - sub + sliding window mean   Matthew Hannah
• [BioC] mva.pairs parameters   Beth Wilmot
• [BioC] mva.pairs parameters   James W. MacDonald
• [BioC] mva.pairs parameters   Beth Wilmot
• [BioC] kyte and doolittle hydropathy values/plot - sub + sliding window mean   Matthew Hannah
• [BioC] Sequence data from Probes   hrishikesh deshmukh
• [BioC] Limma and limmaGUI with Imagene files, problems/bugs report   Dr. Ir. B. van Breukelen
• [BioC] differential expression test   Auer Michael
• [BioC] RE: correcting for 3' bias in highly amplified RNA samples   Wittner, Ben
• [BioC] [COURSE] Computational and Statistical Aspects of Microarray Analysis (III)   stefano iacus
• [BioC] aCGH problem   Christopher, Neil (NIH/NCI)
• [BioC] error in ygs98cdf environment?   Straubhaar, Juerg
• [BioC] bioconductor on xserve   Guoneng Zhong
• [BioC] subsetting exprsSet   Beth Wilmot
• [BioC] error in ygs98cdf environment?   Crispin Miller
• [BioC] bioconductor on xserve   Colin Smith
• [BioC] differential expression test   Gordon K Smyth
• [BioC] QC stats plot   Claudio Lottaz
• [BioC] alt cdf env probe index config problem   Rhonda DeCook
• [BioC] QC stats plot   Robert Gentleman
• [BioC] A question about lowess normalization   Tony Kowal
• [BioC] Could I subset an AffyBatch object by part of probes for each probeset?   Frank Duan
• [BioC] A question about lowess normalization   michael watson (IAH-C)
• [BioC] A question about lowess normalization   Gustavo Henrique Esteves
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Benjamin Haibe-Kains
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   michael watson (IAH-C)
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Benjamin Haibe-Kains
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Antoine Lucas
• [BioC] Handling "nested" factors in limma   michael watson (IAH-C)
• [BioC] A question about lowess normalization   Gordon K Smyth
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   michael watson (IAH-C)
• [BioC] unbalanced design   Arne.Muller at aventis.com
• [BioC] AffyRNAdeg slopes   Vawter, Marquis
• [BioC] AffyRNAdeg slopes   James W. MacDonald
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Charles C. Berry
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Tan, MinHan
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Benjamin Haibe-Kains
• [BioC] Quastion   mohammad mahdi naghizadeh jahr
• [BioC] Could anyone tell me where I could find a large Affymetrix time-series data?   Frank Duan
• [BioC] hclust and (Eisen+ de Hoon) cluster3 program   Wittner, Ben
• [BioC] Bug in normalizeBetweenArrays, method="Rquantile"   Marcus Davy
• [BioC] unbalanced design   Gordon Smyth
• [BioC] Handling "nested" factors in limma   Gordon Smyth
• [BioC] Re: Bug in normalizeBetweenArrays, method="Rquantile"   Gordon Smyth
• [BioC] Having problem with the installation   Ankur Kapil
• [BioC] gene classification problem   Kimpel, Mark W
• [BioC] Having problem with the installation   Jeff Gentry
• [BioC] normalizaton between studies   Arne.Muller at aventis.com
• [BioC] gene classification problem   Charles C. Berry
• [BioC] gene classification problem   Charles C. Berry
• [BioC] limma 2*2 factorial design contrast matrix   Na, Ren
• [BioC] Having problem with the installation   Marcus Davy
• [BioC] Detection p-values in simpleaffy   Crispin Miller
• [BioC] GCRMA and Affymetrix spikeIn hgu133a   Raffaele Calogero
• R: [BioC] GCRMA and Affymetrix spikeIn hgu133a   Alberto Goldoni
• [BioC] Limma FDR question   M PEREZ
• [BioC] Limma FDR question   Sean Davis
• [BioC] Limma FDR question   Ramon Diaz-Uriarte
• [BioC] normalizaton between studies   Anja.von.Heydebreck at merck.de
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Glynn, Earl
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Robert Gentleman
• [BioC] automatic data package maker   Rafael A. Irizarry
• [BioC] automatic data package maker   Tomas Radivoyevitch
• [BioC] automatic data package maker   Robert Gentleman
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Glynn, Earl
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Gordon K Smyth
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Gordon K Smyth
• [BioC] Need better quality control for reliable installation of bioconductor packages?   Robert Gentleman
• [BioC] normalizing data from Afymetrix   Raouf Alami
• [BioC] normalizing data from Afymetrix   James MacDonald
• [BioC] Common microarray clustering method   Ilya Venger
• [BioC] Common microarray clustering method   Mourad Atlas
• [BioC] automatic data package maker   Wolfgang Huber
• [BioC] LGPL C++ source code available from Affy for reading their file f ormats   Wittner, Ben
• [BioC] problem in limmaGUI with Heat Diagram   Dr. Ir. B. van Breukelen
• [BioC] Common microarray clustering method   Jenny Bryan
• [BioC] Affymetrix file parsers released under LGPL open source license   Lelivelt, Mike
• [BioC] limma for R 1.9.1   Gordon Smyth
• [BioC] ecoli2cdf   Wenbin Wei
• [BioC] Agilent data with limmaGUI   宮本 真理
• [BioC] Limma error   Saurin Jani
• [BioC] limma object column subsetting   Matt McCall
• [BioC] (no subject)   Liviu M Vladutu
• [BioC] Problem with limma backgroundCorrect function   michael_kirk at wmi.usyd.edu.au
• [BioC] Agilent data with limmaGUI   James Wettenhall
• [BioC] Agilent data with limmaGUI   Mari Miyamoto
• [BioC] makecdfenv windows XP   Malick Paye
• [BioC] limma object column subsetting   Gordon K Smyth
• [BioC] Problem with limma backgroundCorrect function   Gordon K Smyth
• [BioC] Limma error   Gordon K Smyth
• [BioC] (no subject)   Robert Gentleman
• [BioC] plclust   Auer Michael
• [BioC] makecdfenv windows XP   James W. MacDonald
• [BioC] Common procedure for analysis of cDNA microarray using bioconductor   Yanqin Yang
• [BioC] Affymetrix file parsers released under LGPL open source license   Harry Mangalam
• [BioC] Common procedure for analysis of cDNA microarray using bioconductor   Saurin D. Jani
• [BioC] installing R2....   Raouf Alami
• [BioC] installing R2....   Kasper Daniel Hansen
• [BioC] Affymetrix file parsers released under LGPL open source license   Byron Ellis
• [BioC] Affymetrix file parsers released under LGPL open source license   Harry Mangalam
• [BioC] Affymetrix file parsers released under LGPL open source license   Richard Finney
• [BioC] problem in limmaGUI with Heat Diagram   James Wettenhall
• [BioC] Problems with packages: annaffy, GO, KEGG, golubEsets   Vitalina Komashko
• [BioC]: Clustering with Diana   Anthony Bosco
• [BioC] Common procedure for analysis of cDNA microarray using bioconductor   Sean Davis
• [BioC] Incorrect permissions to edit database package   michael watson (IAH-C)
• [BioC] (no subject)   Saurin D. Jani
• [BioC] Incorrect permissions to edit database package   Jeff Gentry
• [BioC]: Clustering with Diana   Jenny Bryan
• [BioC] pathway analysis package   Josephine Liang
• [BioC]: Clustering with Diana   Chris Wilkinson
• [BioC] pathway analysis package   Robert Gentleman
• [BioC] Problems with packages: annaffy, GO, KEGG, golubEsets   Robert Gentleman
• [BioC]:Export 1 way cluster to treeview   Anthony Bosco
• [BioC] Maybe a usefull for limma users   Dr. Ir. B. van Breukelen
• [BioC] pathway analysis package   Saurin D. Jani
• [BioC] cdf environment for Yeast 2.0 array   Jakub Orzechowski Westholm
• [BioC] pathway analysis package   Sean Davis
• [BioC] pathway analysis package   Josephine Liang
• [BioC] pathway analysis package   John Zhang
• [BioC] pathway analysis package   Sean Davis
• [BioC] Annotation of yeast "ygs98" chip   Xinghua Lu
• [BioC] Limma FDR and p.value   Saurin Jani
• [BioC] uninstalling   Law, Annie
• [BioC] FW: uninstalling   Law, Annie
• [BioC] FW: uninstalling   James W. MacDonald
• [BioC] FW: uninstalling   Jeff Gentry
• [BioC] uninstalling   Seth Falcon
• [BioC] Metrology for Gene Expression -- Postdoc Opportunities at NIST   Marc Salit
• [BioC] Annotation of yeast "ygs98" chip   John Zhang
• [BioC] Maybe a usefull for limma users   Gordon K Smyth
• [BioC] batch vs interactive behavior of reposTools()   Marion Hakanson
• [BioC] Re: Bioconductor Digest, Vol 22, Issue 18   Gordon K Smyth
• [BioC] Problem with aafSymbol   Jeff Lande
• [BioC] limma, FDR, and p.adjust   Kimpel, Mark W
• [BioC] FW: uninstalling   Jan T. Kim
• [BioC] limma, FDR, and p.adjust   Marcus Davy
• [BioC] Normalization based on PM values only   narinder.singh
• [BioC] limma, FDR, and p.adjust   Gordon K Smyth
• [BioC] CEL + BPMAP files for Affymetrix tiling arrays   Sunduz Keles
• [BioC] Using different processed data in limma package   Mari Miyamoto
• [BioC] Using different processed data in limma package   Mari Miyamoto
• [BioC] Re: HGU95a and HGU95av2 with gcrma and combineAffybatch   Vincent Detours
• [BioC] ll.htmlpage question   Fátima Núñez
• [BioC] RE: Bioconductor Digest, Vol 22, Issue 21   Jiuzhou song
• [BioC] RE: Bioconductor Digest, Vol 22, Issue 21   Jiuzhou song
• [BioC] F-tests for factorial effects - limma   Naomi Altman
• [BioC] Using different processed data in limma package   Marcus Davy
• [BioC] ll.htmlpage question   Wolfgang Huber
• [BioC] F-tests for factorial effects - limma   Gordon K Smyth
• [BioC] GoHyperG   Sean Davis
• [BioC] Import of high resolution .CEL files   Soumyaroop Bhattacharya
• [BioC] Using different processed data in limma package   Giovanni Coppola
• [BioC] cDNA raw data   Srinivas Iyyer
• [BioC] cDNA raw data   michael watson (IAH-C)
• [BioC] cDNA raw data   Sean Davis
• [BioC] Re: GoHyperG   Nicholas Lewin-Koh
• [BioC] Re: GoHyperG   Sean Davis
• [BioC] Re: GoHyperG   Nicholas Lewin-Koh
• [BioC] Installing Bioconductor under   John Cornell
• [BioC] Error setting boxplot title in Affy   Paul Boutros
• [BioC] reading Agilent data files   Olivier BUHARD
• [BioC] problems with affy & widgets   Edoardo Saccenti
• [BioC] problems with affy & widgets   Edoardo Saccenti
• [BioC] Error setting boxplot title in Affy   James MacDonald
• [BioC] Installing Bioconductor under   Gentleman
• [BioC] GEO soft files   Edoardo Saccenti
• [BioC] GEO soft files   Sean Davis
• [BioC] GEO soft files   Edoardo Saccenti
• [BioC] Testing two hypothesis by linear models   Ron Ophir
• [BioC] Siggenes output only gives NAs?   Tiago R Magalhaes
• [BioC] XML Package   Edoardo Saccenti
• [BioC] XML Package   Jeff Gentry
• [BioC] XML Package   John Zhang
• [BioC] XML Package   Tomas Radivoyevitch
• [BioC] SKY/CGH data. How do I interpret it.   S Peri
• [BioC] persistent errors   Edoardo Saccenti
• [BioC] SKY/CGH data. How do I interpret it.   Luzie U. Wingen
• [BioC] Configuration of memory usage   Tae-Hoon Chung
• [BioC] Re: [R] Configuration of memory usage   Peter Dalgaard
• [BioC] fixed problem with libxml   Edoardo Saccenti
• [BioC] Sequence data and filtering   hrishikesh deshmukh
• [BioC] (no subject)   Lana Schaffer
• [BioC] assigning intensity values   Lana Schaffer
• [BioC] assigning intensity values   James MacDonald
• [BioC] writing out a celfile   Lana Schaffer
• [BioC] Reading flag data from Agilent files   Olivier BUHARD
• [BioC] writing out a celfile   Rafael Irizarry
• [BioC] issue in arrayQuality package   Longsi Ran
• [BioC] issue in arrayQuality package   Jean Yee Hwa Yang
• [BioC] issue in arrayQuality package   Jean Yee Hwa Yang
• [BioC] issue in arrayQuality package   Longsi Ran
• [BioC] issue in arrayQuality package   Longsi Ran
• [BioC] Beginner help   Toni-Ann Mistretta
• [BioC] Beginner help   Jeff Gentry
• [BioC] Beginner help   Toni-Ann Mistretta
• [BioC] Beginner help   James MacDonald
• [BioC] Beginner help   Vincent Carey 525-2265
• [BioC] Beginner help   Toni-Ann Mistretta
• [BioC] Beginner help   James MacDonald
• [BioC] Sequence data and filtering   Justin Borevitz

Last message date: Fri Dec 31 06:39:30 CEST 2004
Archived on: Sun Jan 2 20:25:37 CEST 2005

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