April 2006 Archives by author

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Starting: Sat Apr 1 00:21:12 CEST 2006
Ending: Sun Apr 30 09:32:27 CEST 2006
Messages: 304

• [BioC] Error with GEOquery   Peter (BioC)
• [BioC] Searching for data in data.frames   michael watson (IAH-C)
• [BioC] Limma: background correction. Use or ignore?   Naomi Altman
• [BioC] urgent..   Naomi Altman
• [BioC] Limma vs anova (GeneSpring)   Naomi Altman
• [BioC] differentially expressed genes with limma   Naomi Altman
• [BioC] differentially expressed genes with limma   Naomi Altman
• [BioC] differentially expressed genes with limma   Naomi Altman
• [BioC] differentially expressed genes with limma   Naomi Altman
• [BioC] Removing probes before or after normalization   Naomi Altman
• [BioC] 2x2 factorial loop without common reference (pool)   Naomi Altman
• [BioC] 2x2 factorial loop without common reference (pool)   Naomi Altman
• [BioC] invariant set normalisation   Naomi Altman
• [BioC] Problems using text to subset array information from anexpression set   Alvord, Greg (DMS) [Contr]
• [BioC] internet2.dll equivalent for Mac   Jonathan Arthur
• [BioC] R crashes on winXP with 2G memory   Henrik Bengtsson
• [BioC] Limma: background correction. Use or ignore?   Henrik Bengtsson
• [BioC] Limma: background correction. Use or ignore?   Henrik Bengtsson
• [BioC] request for gtype_cel_to_pq   Dick Beyer
• [BioC] Affymetrix exon arrays?   Ben Bolstad
• [BioC] R crashing, updating   Ben Bolstad
• [BioC] Removing probes before or after normalization   Bornman, Daniel M
• [BioC] Global extreme changes   Pedro Botías
• [BioC] custom cdf files with just.gcrma   D C
• [BioC] affy package and porcine arrays   David Carter
• [BioC] affy package and porcine arrays   David Carter
• [BioC] Problems using text to subset array information from an expression set   Benilton Carvalho
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Benilton Carvalho
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Benilton Carvalho
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Benilton Carvalho
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Benilton Carvalho
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Benilton Carvalho
• [BioC] AffylmGUI   Chen, Kegui
• [BioC] AffylmGUI   Chen, Kegui
• [BioC] Need help on understanding this error message   Fang Cheng
• [BioC] Limma: combining 2 microarray studies   Ana Conesa
• [BioC] Limma: combining 2 microarray studies   Ana Conesa
• [BioC] cross-species affy analysis   Sean Davis
• [BioC] FW: AnnBuilder package and URLs   Sean Davis
• [BioC] problem with GEOquery   Sean Davis
• [BioC] Error with GEOquery   Sean Davis
• [BioC] Error with GEOquery   Sean Davis
• [BioC] Wilcoxon rank sum test on Golub dataset   Sean Davis
• [BioC] Duplicated probesets for the same gene   Sean Davis
• [BioC] How use the function "normalizeWithinArrays" with loess in limma   Sean Davis
• [BioC] data with known expressed genes   Sean Davis
• [BioC] (no subject)   Hrishikesh Deshmukh
• [BioC] scatterplot3d?!   Hrishikesh Deshmukh
• [BioC] pm() mm() functionality changed?   Dmitry
• [BioC] pm() mm() functionality changed?   Dmitry
• [BioC] pm() mm() functionality changed?   Dmitry
• [BioC] error in mas5calls() for soybean chip   Jenny Drnevich
• [BioC] error in mas5calls() for soybean chip   Jenny Drnevich
• [BioC] Removing probes before or after normalization   Jenny Drnevich
• [BioC] When to treat technical reps as biological reps? WAS:Re: 2x2 factorial loop without common reference (pool)   Jenny Drnevich
• [BioC] CodeLink Package: Not a Codelink exported file.   Diego Díez
• [BioC] Problem with metadata   Claudia Döring
• [BioC] R CMD --args   D.Enrique ESCOBAR ESPINOZA
• [BioC] update.packages with bioconductor   D.Enrique ESCOBAR ESPINOZA
• [BioC] internet2.dll equivalent for Mac   Byron Ellis
• [BioC] Classification and the Golub data set   Chelsea Ellis
• [BioC] Type I and Type II errors: Multiple Testing   Mohammad Esad-Djou
• [BioC] internet2.dll equivalent for Mac   Seth Falcon
• [BioC] Affychip coli asv2 annotation files   Seth Falcon
• [BioC] Rgraphviz install problem   Seth Falcon
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Seth Falcon
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Seth Falcon
• [BioC] R CMD --args   Seth Falcon
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Seth Falcon
• [BioC] R crashing, updating   Seth Falcon
• [BioC] R, R scripting and shell   Seth Falcon
• [BioC] hgu133plus2 GO issues   Seth Falcon
• [BioC] RBGL package   Seth Falcon
• [BioC] Problem installing hexbin?   Seth Falcon
• [BioC] Thoughts on computer purchase   Seth Falcon
• [BioC] Problem installing hexbin?   Seth Falcon
• [BioC] Bioconductor 1.8 for R 2.3.0 is released!   Seth Falcon
• [BioC] invariant set normalisation   Seth Falcon
• [BioC] Thoughts on computer purchase   Seth Falcon
• [BioC] What's new in the graph package   Seth Falcon
• [BioC] Problem installing hexbin?   Seth Falcon
• [BioC] error running the example of the widget function in the widgetTools library   Seth Falcon
• [BioC] B value cutoff in LIMMA   Richard Friedman
• [BioC] Problem installing hexbin?   Robert Gentleman
• [BioC] yet another question on technical replicates...   Giorgi, Elena
• [BioC] Hot to find gene names and descriptions from accession numbers ?   Giulio Di Giovanni
• [BioC] problem with GEOquery   Alberto Goldoni
• [BioC] problem with GEOquery   Alberto Goldoni
• [BioC] GEOquery problems   Alberto Goldoni
• [BioC] merge SMD data from different print batch   Jeremy Gollub
• [BioC] cross-species affy analysis   Dario Greco
• [BioC] U133A probe sequences...?   Dario Greco
• [BioC] UseMart not working   HFL
• [BioC] Thoughts on computer purchase   Marion Hakanson
• [BioC] Fusarium CDF   Heather Erika Hallen
• [BioC] Problems using text to subset array information from an expression set   Kasper Daniel Hansen
• [BioC] Problems using text to subset array information from an expression set   Kasper Daniel Hansen
• [BioC] Building BioC packages from source on MacOSX (R-2.3.0)   Kasper Daniel Hansen
• [BioC] Need help on understanding this error message   Kasper Daniel Hansen
• [BioC] Administrative Rigths   Kasper Daniel Hansen
• [BioC] Classification and the Golub data set   Christos Hatzis
• [BioC] Problem installing hexbin?   David Henderson
• [BioC] Problem installing hexbin?   David Henderson
• [BioC] [Fwd: Re: Problem installing hexbin?]   David Henderson
• [BioC] Classification and the Golub data set   Stephen Henderson
• [BioC] [R] Cross validation reviews   Stephen Henderson
• [BioC] Searching for data in data.frames   Stephen Henderson
• [BioC] function checkfac in rowttests   Wolfgang Huber
• [BioC] installation permisssions   Wolfgang Huber
• [BioC] Administrative Rigths   Wolfgang Huber
• [BioC] biomaRt and ensembl tables   Wolfgang Huber
• [BioC] invariant set normalisation   Al Ivens
• [BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available   Srinivas Iyyer
• [BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available   Srinivas Iyyer
• [BioC] CodeLink Package: Not a Codelink exported file.   Srinivas Iyyer
• [BioC] hgu133plus2 GO issues   Jake
• [BioC] hgu133plus2 GO issues   Jake
• [BioC] Thoughts on computer purchase   Jake
• [BioC] Limma vs anova (GeneSpring)   Wettenhall James
• [BioC] Limma vs anova (GeneSpring)   Wettenhall James
• [BioC] Limma; Background and Single Channel Analysis   Simone de Jong
• [BioC] Global extreme changes   ELENITA KANIN
• [BioC] Wilcoxon rank sum test on Golub dataset   Andrej Kastrin
• [BioC] "One Way ANOVA" with limma   Max Kauer
• [BioC] Predicting number of replicates   Khan, Sohail
• [BioC] Predicting number of replicates   Khan, Sohail
• [BioC] affycoretools limma2annaffy fold change output question   Kimpel, Mark William
• [BioC] function checkfac in rowttests   Matthias Kohl
• [BioC] function "checkfac" in package "genefilter"   Matthias Kohl
• [BioC] PhD Student Position in Statistics in Switzerland on Bayesian Methods for Integrated Genomics   Ivo Kwee
• [BioC] Problems using text to subset array information from an expression set   Jeff Lande
• [BioC] Problems using text to subset array information from an expression set   Jeff Lande
• [BioC] A questions related to affymetrix chip normalization from multiple platform   Li, Aiguo (NIH/NCI) [C]
• [BioC] A questions related to affymetrix chip normalizationfrom multiple platform   Li, Aiguo (NIH/NCI) [C]
• [BioC] running AnnBuilder Vignette:Error in baseFile   Xue Lin
• [BioC] A limma question.   Johan Lindberg
• [BioC] Different results from two separate comparisons   Delong Liu
• [BioC] AnnBuilder package and URLs   Ting-Yuan Liu
• [BioC] AFFX-BioB-3_at annotation   Ting-Yuan Liu
• [BioC] AFFX-BioB-3_at annotation   Ting-Yuan Liu
• [BioC] Problem with metadata   Ting-Yuan Liu
• [BioC] differentially expressed genes with limma   Lisa Luo
• [BioC] differentially expressed genes with limma   Lisa Luo
• [BioC] differentially expressed genes with limma   Lisa Luo
• [BioC] differentially expressed genes with limma   Lisa Luo
• [BioC] Classification and the Golub data set   James W. MacDonald
• [BioC] pm() mm() functionality changed?   James W. MacDonald
• [BioC] pm() mm() functionality changed?   James W. MacDonald
• [BioC] affy package and porcine arrays   James W. MacDonald
• [BioC] limma toptable missing ProbeId/ documentation question   James W. MacDonald
• [BioC] limma toptable missing ProbeId/ documentation question   James W. MacDonald
• [BioC] Plotting symbols for MA plot in Affycomp   James W. MacDonald
• [BioC] yet another question on technical replicates...   James W. MacDonald
• [BioC] AffylmGUI   James W. MacDonald
• [BioC] Searching vignette   James W. MacDonald
• [BioC] urgent..   James W. MacDonald
• [BioC] errors when trying to load CEL files   James W. MacDonald
• [BioC] hgu133plus2 GO issues   James W. MacDonald
• [BioC] hgu133plus2 GO issues   James W. MacDonald
• [BioC] error in mas5calls() for soybean chip   James W. MacDonald
• [BioC] affycoretools limma2annaffy fold change output question   James W. MacDonald
• [BioC] U133A probe sequences...?   James W. MacDonald
• [BioC] normalizing with different RNAdeg slopes   James W. MacDonald
• [BioC] Fusarium CDF   James W. MacDonald
• [BioC] Duplicated probesets for the same gene   James W. MacDonald
• [BioC] custom cdf files with just.gcrma   James W. MacDonald
• [BioC] Limma User's Guide Example of design matrices   James W. MacDonald
• [BioC] golubEset   James W. MacDonald
• [BioC] Micro-RNA research   McGee, Monnie
• [BioC] Cross validation reviews   McGee, Monnie
• [BioC] Plotting symbols for MA plot in Affycomp   McGee, Monnie
• [BioC] R CMD --args   Steffen Moeller
• [BioC] Duplicated probesets for the same gene   Saroj Mohapatra
• [BioC] Duplicated probesets for the same gene   Saroj Mohapatra
• [BioC] AnnBuilder package and URLs   Tabare Mourot
• [BioC] R crashing, updating   Tarun Nayar
• [BioC] normalizing with different RNAdeg slopes   Tarun Nayar
• [BioC] normalizing with different RNAdeg slopes   Tarun Nayar
• [BioC] Searching vignette   Robert Olaso
• [BioC] Problem installing hexbin?   Sander Oom
• [BioC] Problem installing hexbin?   Sander Oom
• [BioC] Problem installing hexbin?   Sander Oom
• [BioC] Rgraphviz install problem   Herve Pages
• [BioC] R crashing, updating   Herve Pages
• [BioC] update.packages with bioconductor   Herve Pages
• [BioC] Thoughts on computer purchase   Lance Palmer
• [BioC] MEEBO-tool in arrayQuality   Paquet, Agnes
• [BioC] Global extreme changes   Alexander Ploner
• [BioC] Affymetrix exon arrays?   Johannes Rainer
• [BioC] merge SMD data from different print batch   Adaikalavan Ramasamy
• [BioC] merge SMD data from different print batch   Adaikalavan Ramasamy
• [BioC] LIMMA: testing for batch effects   Adaikalavan Ramasamy
• [BioC] LIMMA:design and contrast matrices for biological and technical replicates   Adaikalavan Ramasamy
• [BioC] A questions related to affymetrix chip normalization from multiple platform   Adaikalavan Ramasamy
• [BioC] Predicting number of replicates   Adaikalavan Ramasamy
• [BioC] urgent..   Adaikalavan Ramasamy
• [BioC] BioC] using limma with no replicates   Pedro Lopez Romero
• [BioC] blocking using limma   Pedro López Romero
• [BioC] Duplicated probesets for the same gene   David Ruau
• [BioC] CFP: Distributed, High-Performance and Grid Computing in Computational Biology   Hershel Safer
• [BioC] Compiling RMAGEML 2.5.3 or 2.4.0 under Mac OS X 10.4.5 fails   Marc Saric
• [BioC] Compiling RMAGEML 2.5.3 or 2.4.0 under Mac OS X 10.4.5 fails (not anymore)   Marc Saric
• [BioC] Thoughts on computer purchase   Lana Schaffer
• [BioC] R-Fest: Workshops on S, R and Bioconductor   David Scott
• [BioC] Affymetrix exon arrays?   Michael Seewald
• [BioC] Error with GEOquery   Sharon
• [BioC] Error with GEOquery   Sharon
• [BioC] Error with GEOquery   Sharon
• [BioC] R CMD --args   Weiwei Shi
• [BioC] sample size estimation for microarray data classification or model performance evaluation   Weiwei Shi
• [BioC] golubEset   Silveira, Lori
• [BioC] error in mas5calls() for soybean chip   Ken Simpson
• [BioC] pamr package: pamr.adaptthresh()   Tim Smith
• [BioC] BioC] using limma with no replicates   Gordon Smyth
• [BioC] LIMMA: choice of offset value for background correction method "normexp"   Gordon Smyth
• [BioC] Limma: background correction. Use or ignore?   Gordon Smyth
• [BioC] B value cutoff in LIMMA   Gordon Smyth
• [BioC] Limma: How to read gene list, coordinates of sport when NO GAL file available   Gordon Smyth
• [BioC] Fwd: Limma: How to read gene list, coordinates of sport when NO GAL file available   Gordon Smyth
• [BioC] Different results Limma vs LimmaGUI?   Gordon Smyth
• [BioC] AffylmGUI   Gordon Smyth
• [BioC] LIMMA: testing for batch effects   Gordon Smyth
• [BioC] AffylmGUI   Gordon Smyth
• [BioC] Limma: correct calculation of B statistics (log odds)   Gordon Smyth
• [BioC] Limma: correct calculation of B statistics (log odds)   Gordon Smyth
• [BioC] Limma: correct calculation of B statistics (log odds)   Gordon Smyth
• [BioC] A limma question   Gordon Smyth
• [BioC] 2x2 factorial loop without common reference (pool)   Gordon Smyth
• [BioC] Limma: correct calculation of B statistics (log odds)   Gordon Smyth
• [BioC] Memory issues with limma and ImaGen file import   Gordon Smyth
• [BioC] Limma: background correction. Use or ignore?   Gordon K Smyth
• [BioC] Rgraphviz install problem   Shamit Soneji
• [BioC] Memory issues with limma and ImaGen file import   Christian Spieth
• [BioC] RBGL package   Jing Su
• [BioC] biomaRt and ensembl tables   TM
• [BioC] biomaRt and ensembl tables   TM
• [BioC] limma toptable missing ProbeId/ documentation question   Björn Usadel
• [BioC] toptable missing ProbeId/ documentation question   Björn Usadel
• [BioC] Problem with metadata   Björn Usadel
• [BioC] Wilcoxon rank sum test on Golub dataset   Björn Usadel
• [BioC] invariant set normalisation   Sally-Ann Walford
• [BioC] errors when trying to load CEL files   Wall, Dennis Paul
• [BioC] errors when trying to load CEL files   Wall, Dennis Paul
• [BioC] LIMMA:design and contrast matrices for biological and technical replicates   Mike White
• [BioC] LIMMA:design and contrast matrices for biological and technical replicates   Mike White
• [BioC] Limma User's Guide Example of design matrices   Mike White
• [BioC] Limma: correct calculation of B statistics (log odds)   Wittner, Ben, Ph.D.
• [BioC] Limma: correct calculation of B statistics (log odds)   Wittner, Ben, Ph.D.
• [BioC] webbioc   Matthias Wittwer
• [BioC] AFFX-BioB-3_at annotation   Wu, Xiwei
• [BioC] AFFX-BioB-3_at annotation   Wu, Xiwei
• [BioC] MAQC at FDA   Wu, Xiwei
• [BioC] U133A probe sequences...?   Zhijin (Jean) Wu
• [BioC] Duplicated probesets for the same gene   Ye, Bin
• [BioC] Limma, marray and Agilent 44K   Nataliya Yeremenko
• [BioC] limma, marray and Agilent 44K   Nataliya Yeremenko
• [BioC] Thoughts on computer purchase   Yoder, Sean J.
• [BioC] Thoughts on computer purchase   Yoder, Sean J.
• [BioC] R installation error----please help   Zhang, Jacob
• [BioC] data with known expressed genes   Tony Zheng
• [BioC] Gene-GO   narinder.singh at diagenic.com
• [BioC] Gene-GO   sdurinck at ebi.ac.uk
• [BioC] biomaRt and ensembl tables   sdurinck at ebi.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: combining 2 microarray studies   J.delasHeras at ed.ac.uk
• [BioC] Limma: combining 2 microarray studies   J.delasHeras at ed.ac.uk
• [BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available   J.delasHeras at ed.ac.uk
• [BioC] Different results Limma vs LimmaGUI?   J.delasHeras at ed.ac.uk
• [BioC] Different results Limma vs LimmaGUI?   J.delasHeras at ed.ac.uk
• [BioC] Limma: background correction. Use or ignore?   J.delasHeras at ed.ac.uk
• [BioC] Limma: correct calculation of B statistics (log odds)   J.delasHeras at ed.ac.uk
• [BioC] Searching for data in data.frames   J.delasHeras at ed.ac.uk
• [BioC] Limma: correct calculation of B statistics (log odds)   J.delasHeras at ed.ac.uk
• [BioC] Limma: correct calculation of B statistics (log odds)   J.delasHeras at ed.ac.uk
• [BioC] Searching for data in data.frames   J.delasHeras at ed.ac.uk
• [BioC] Searching for data in data.frames   J.delasHeras at ed.ac.uk
• [BioC] Question about topTable output formatting (Limma) in Excel   J.delasHeras at ed.ac.uk
• [BioC] Question about topTable output formatting (Limma) in Excel   J.delasHeras at ed.ac.uk
• [BioC] Limma; Background and Single Channel Analysis   J.delasHeras at ed.ac.uk
• [BioC] Limma User's Guide Example of design matrices   kfbargad at ehu.es
• [BioC] Affychip coli asv2 annotation files   lemerle at embl.de
• [BioC] sample size estimation for microarray data classification or model performance evaluation   Malick.PAYE at eu.biomerieux.com
• [BioC] 2x2 factorial loop without common reference (pool)   francois fauteux
• [BioC] 2x2 factorial loop without common reference (pool)   francois fauteux
• [BioC] R installation error----please help   hpages at fhcrc.org
• [BioC] webbioc   kirk hammet
• [BioC] internet2.dll equivalent for Mac   stefano iacus
• [BioC] urgent..   kst
• [BioC] urgent..   kst
• [BioC] installation permisssions   claudio.is at libero.it
• [BioC] R, R scripting and shell   claudio.is at libero.it
• [BioC] Administrative Rigths   marco_oliviero77
• [BioC] error running the example of the widget function in the widgetTools library   mattia
• [BioC] PLIER   sandhyakiran pemmasani
• [BioC] Reg: PLIER   sandhyakiran pemmasani
• [BioC] Plotting error after quality control   marco scandroglio
• [BioC] [R] Cross validation reviews   portnoy at supereva.it
• [BioC] How use the function "normalizeWithinArrays" with loess in limma   sysra
• [BioC] How use the function "normalizeWithinArrays" with loess in limma   sysra
• [BioC] difference Between ANOVA 2 way and Factors effect model and fews questions   gregory voisin

Last message date: Sun Apr 30 09:32:27 CEST 2006
Archived on: Fri Jun 2 23:41:27 CEST 2006

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