December 2006 Archives by date

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Starting: Fri Dec 1 02:33:10 CET 2006
Ending: Sat Dec 30 02:42:15 CET 2006
Messages: 327

• [BioC] Some Genefilter questions   David K Pritchard
• [BioC] LIMMA makeContrasts question   T S
• [BioC] fetch filen names   James W. MacDonald
• [BioC] Probe Interrogation Positions of Affy chips   botto
• [BioC] How to get the number of Stat pairs used in MAS5   James W. MacDonald
• [BioC] Some Genefilter questions   Claus Mayer
• [BioC] Probe Interrogation Positions of Affy chips   James W. MacDonald
• [BioC] Some Genefilter questions   James W. MacDonald
• [BioC] webbioc install on linux redhat FC4   haiyan wu
• [BioC] Limma with block and replicate measurement   Yanyan Li
• [BioC] analyzing genomic hybridization data with limma?   Erik Dopman
• [BioC] Limma with block and replicate measurement   Yanyan Li
• [BioC] Some Genefilter questions   Jenny Drnevich
• [BioC] Some Genefilter questions   Robert Gentleman
• [BioC] OPERON human v3 library   Nianhua Li
• [BioC] GOstat   Seth Falcon
• [BioC] 2fold sigchanges from limma   Ivan Baxter
• [BioC] How to get the number of Stat pairs used in MAS5   Julie Dickerson
• [BioC] limma duplicateCorrelation question   Karen Vranizan
• [BioC] How to get the number of Stat pairs used in MAS5   James W. MacDonald
• [BioC] BIRD 07 call for particpation   Prof. Roland Wagner
• [BioC] 2fold sigchanges from limma   James W. MacDonald
• [BioC] Comparing to background   Wolfgang Huber
• [BioC] Integrating FOSS genomics and FOSS clinical applications   Fred Trotter
• [BioC] limma duplicateCorrelation question   Gordon Smyth
• [BioC] Limma with block and replicate measurement   Gordon Smyth
• [BioC] LIMMA makeContrasts question   Gordon Smyth
• [BioC] Greek characters and subscripts in network graphs   Martin Henry H. Stevens
• [BioC] R News, volume 6, issue 5 is now available   Paul Murrell
• [BioC] 2fold sigchanges from limma   Gordon Smyth
• [BioC] error during installation of genefilter package: "no package 'genefilter' at the repositories"   C Carey
• [BioC] Open position "Clinical Genomics Statistician" at Novartis Basel Switzerland   martin.schumacher at novartis.com
• [BioC] snapCGH and CGH method evaluation   João Fadista
• [BioC] Creation of AffyBatch object   Karin Lagesen
• [BioC] LIMMA makeContrasts question   J.delasHeras at ed.ac.uk
• [BioC] snapCGH and CGH method evaluation   Ramon Diaz-Uriarte
• [BioC] Array normalisation with Limma: would this be reasonable?   J.delasHeras at ed.ac.uk
• [BioC] snapCGH and CGH method evaluation   Sean Davis
• [BioC] BIDM Call for papers   Prof. Roland Wagner
• [BioC] Some Genefilter questions   Lourdusamy A Anbarasu
• [BioC] standard deviation from log to normal scale???   Jesper Ryge
• [BioC] Some Genefilter questions   Amy Mikhail
• [BioC] Some Genefilter questions   Jenny Drnevich
• [BioC] Some Genefilter questions   Jenny Drnevich
• [BioC] Some Genefilter questions   Amy Mikhail
• [BioC] Some Genefilter questions   Amy Mikhail
• [BioC] problems with gcrma just.gcrma   Elisabetta Manduchi
• [BioC] question about using maSigPro   James Anderson
• [BioC] analyzing genomic hybridization data with limma?   Sean Davis
• [BioC] error during installation of genefilter package: "no package 'genefilter' at the repositories"   Seth Falcon
• [BioC] problems with gcrma just.gcrma   Seth Falcon
• [BioC] problems with gcrma just.gcrma   James W. MacDonald
• [BioC] Error installing customer created CDF package   Tan, Ruimin
• [BioC] Error installing customer created CDF package   Kasper Daniel Hansen
• [BioC] Question about Li&Wong normalization   Malick.PAYE at eu.biomerieux.com
• [BioC] LIMMA makeContrasts question   kfbargad at ehu.es
• [BioC] retrieving chromosome lengths using biomaRt?   Shamit Soneji
• [BioC] retrieving chromosome lengths using biomaRt?   Sean Davis
• [BioC] Affy! From raw data files to Summary expression value without expresso!   Höning, Gunther
• [BioC] retrieving chromosome lengths using biomaRt?   James W. MacDonald
• [BioC] Affy! From raw data files to Summary expression value without expresso!   James W. MacDonald
• [BioC] problems with gcrma just.gcrma   Elisabetta Manduchi
• [BioC] problems with gcrma just.gcrma   Elisabetta Manduchi
• [BioC] problems with gcrma just.gcrma   James W. MacDonald
• [BioC] RBGL installation on Ubuntu 6.10   lgautier at altern.org
• [BioC] Error installing customer created CDF package   Tan, Ruimin
• [BioC] problems with gcrma just.gcrma   Elisabetta Manduchi
• [BioC] 2x2 factorial with dye effect, limma design   Thomas Degenkolbe
• [BioC] problems with gcrma just.gcrma   James W. MacDonald
• [BioC] problems with gcrma just.gcrma   lgautier at altern.org
• [BioC] standard deviation from log to normal scale???   Wolfgang Huber
• [BioC] GCRMA with HG-U95A and HG-U95Av2   Nicolas STRANSKY
• [BioC] question about maSigPro   James Anderson
• [BioC] Trouble with gcrma background correction   Herve Pages
• [BioC] question about maSigPro   Ana Conesa
• [BioC] read.maimages: median intesities instead of mean   Lakshmanan Iyer
• [BioC] AffyRNAdeg: "degradation" or "digestion"?   Gordon Smyth
• [BioC] Question about Li&Wong normalization   lgautier at altern.org
• [BioC] read.maimages: median intesities instead of mean   Gordon Smyth
• [BioC] AffyRNAdeg: "degradation" or "digestion"?   Robert Gentleman
• [BioC] gcrma background correction   Sucheta Tripathy
• [BioC] Reference on linear models [was LIMMA makeContrasts question]   Gordon Smyth
• [BioC] C/C++ function registration mechanism   Holger Fröhlich
• [BioC] C/C++ function registration mechanism   Oleg Sklyar
• [BioC] Array normalisation with Limma: would this be reasonable?   J.delasHeras at ed.ac.uk
• [BioC] Reference on linear models   Katherine Lawler
• [BioC] converting GEO soft files to MS excel files   Dr_Gyorffy_Balazs
• [BioC] converting GEO soft files to MS excel files   Sean Davis
• [BioC] aCGH across samples   Daniel Brewer
• [BioC] Combining replicate spots in CGH data   João Fadista
• [BioC] converting GEO soft files to MS excel files   Sean Davis
• [BioC] Normalization Between Arrays for common reference, time course and two color direct designs.   Vinoy Kumar Ramachandran
• [BioC] aCGH across samples   Sean Davis
• [BioC] Combining replicate spots in CGH data   Sean Davis
• [BioC] How to use detect call in GCRMA (or RMA) analysis?   Wang mingyi
• [BioC] How to use detect call in GCRMA (or RMA) analysis?   Kasper Daniel Hansen
• [BioC] gcrma background correction   Kasper Daniel Hansen
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Vinoy Kumar Ramachandran
• [BioC] Combining replicate spots in CGH data   Ramon Diaz-Uriarte
• [BioC] Combining replicate spots in CGH data   João Fadista
• [BioC] How to use detect call in GCRMA (or RMA) analysis?   Jianping Jin
• [BioC] RMA normalization and MAS5.0 detection calls   haiyan wu
• [BioC] How to use detect call in GCRMA (or RMA) analysis?   Amit Bahl
• [BioC] Combining replicate spots in CGH data   Ramon Diaz-Uriarte
• [BioC] RMA normalization and MAS5.0 detection calls   James W. MacDonald
• [BioC] out of memory problem using affycoretools   James Anderson
• [BioC] RMA normalization and MAS5.0 detection calls   Naomi Altman
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Jenny Drnevich
• [BioC] RMA normalization and MAS5.0 detection calls   Jenny Drnevich
• [BioC] out of memory problem using affycoretools   Jenny Drnevich
• [BioC] RMA normalization and MAS5.0 detection calls   James W. MacDonald
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Jenny Drnevich
• [BioC] Help:How to do normalization with Ambion bioarray data?   julin at aecom.yu.edu
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Weiyin Zhou
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Vinoy Kumar Ramachandran
• [BioC] RMA normalization and MAS5.0 detection calls - correction   Jenny Drnevich
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Jenny Drnevich
• [BioC] sam question about time course   James Anderson
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Weiyin Zhou
• [BioC] gcrma background correction-saving output   Sucheta Tripathy
• [BioC] comparing different batches of data directly   Sabine Reichelt
• [BioC] Help:How to do normalization with Ambion bioarray data?   Naomi Altman
• [BioC] Help:How to do normalization with Ambion bioarray data?   Al Ivens
• [BioC] out of memory problem using affycoretools   Al Ivens
• [BioC] gcrma background correction-saving output   Lourdusamy A Anbarasu
• [BioC] RMA normalization and MAS5.0 detection calls   Sarwar, Rizwan
• [BioC] RMA normalization and MAS5.0 detection calls   Sean Davis
• [BioC] problems with gcrma just.gcrma   lgautier at altern.org
• [BioC] problems with gcrma just.gcrma   lgautier at altern.org
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   yanju
• [BioC] GCRMA with HG-U95A and HG-U95Av2   Nicolas STRANSKY
• [BioC] comparing different batches of data directly   James W. MacDonald
• [BioC] R-2.4.0/bioconductor/darwin kernel version problem   Charlie Whittaker
• [BioC] R-2.4.0/bioconductor/darwin kernel version problem   Sean Davis
• [BioC] R-2.4.0/bioconductor/darwin kernel version problem   Seth Falcon
• [BioC] comparing different batches of data directly   Kamila Naxerova
• [BioC] GCRMA with HG-U95A and HG-U95Av2   Seth Falcon
• [BioC] gcrma background correction-saving output   Sucheta Tripathy
• [BioC] GCRMA with HG-U95A and HG-U95Av2   Nicolas STRANSKY
• [BioC] GCRMA with HG-U95A and HG-U95Av2   James W. MacDonald
• [BioC] gcrma background correction-saving output   Jenny Drnevich
• [BioC] gcrma background correction-saving output   Sucheta Tripathy
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Jenny Drnevich
• [BioC] Normalization between arrays for common reference, time course and direct two color designs   Jenny Drnevich
• [BioC] out of memory problem using affycoretools   Jenny Drnevich
• [BioC] out of memory problem using affycoretools - correction!   Jenny Drnevich
• [BioC] simpleaffy question   D.Enrique ESCOBAR ESPINOZA
• [BioC] makecdfenv   Wolfgang Huber
• [BioC] simpleaffy question   J.delasHeras at ed.ac.uk
• [BioC] makecdfenv   Martin Morgan
• [BioC] simpleaffy question   James W. MacDonald
• [BioC] simpleaffy question   J.delasHeras at ed.ac.uk
• [BioC] simpleaffy question   James W. MacDonald
• [BioC] How to add additional annotation column in MA.list or results.fit   Vinoy Kumar Ramachandran
• [BioC] How to add additional annotation column in MA.list or results.fit   J.delasHeras at ed.ac.uk
• [BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls   haiyan wu
• [BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls   Morten Mattingsdal
• [BioC] Compare results from different analysis (Affymetrix)   Ingrid H. G. Østensen
• [BioC] Compare results from different analysis (Affymetrix)   Sean Davis
• [BioC] Compare results from different analysis (Affymetrix)   James W. MacDonald
• [BioC] How to add additional annotation column in MA.list orresults.fit   J.Oosting at lumc.nl
• [BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls   lgautier at altern.org
• [BioC] chip area distortion tolerance   D.Enrique ESCOBAR ESPINOZA
• [BioC] variation in output -using gcrma: bg correction   Sucheta Tripathy
• [BioC] variation in output -using gcrma: bg correction   James W. MacDonald
• [BioC] chip area distortion tolerance   Thalacker-Mercer, Anna E
• [BioC] Odds Ratio in GOstat   Naomi Altman
• [BioC] Odds Ratio in GOstat   James W. MacDonald
• [BioC] Odds Ratio in GOstat   Seth Falcon
• [BioC] makecdfenv   Martin Morgan
• [BioC] Odds Ratio in GOstat   Naomi Altman
• [BioC] Odds Ratio in GOstat   Naomi Altman
• [BioC] Odds Ratio in GOstat   Seth Falcon
• [BioC] Odds Ratio in GOstat [resolved?]   Seth Falcon
• [BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls   Kasper Daniel Hansen
• [BioC] Odds Ratio in GOstat [resolved?]   Naomi Altman
• [BioC] silly lm and anova question   James Anderson
• [BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls   haiyan wu
• [BioC] silly lm and anova question   Wolfgang Huber
• [BioC] Compare results from different analysis (Affymetrix)   Ingrid H. G. Østensen
• [BioC] Odds Ratio in GOstat [resolved?]   Björn Usadel
• [BioC] silly lm and anova question   Pedro López Romero
• [BioC] Compare results from different analysis (Affymetrix)   Sean Davis
• [BioC] chip area distortion tolerance   James W. MacDonald
• [BioC] chip area distortion tolerance   James W. MacDonald
• [BioC] Odds Ratio in GOstat [resolved?]   Naomi Altman
• [BioC] Odds Ratio in GOstat [resolved?]   Robert Gentleman
• [BioC] Odds Ratio in GOstat [resolved?]   Sean Davis
• [BioC] makecdfenv   Jenny Drnevich
• [BioC] Odds Ratio in GOstat [resolved?]   Robert Gentleman
• [BioC] makecdfenv   Henrik Bengtsson
• [BioC] Odds Ratio in GOstat [resolved?]   Sean Davis
• [BioC] Separate Channel Analysis of Two-Color Data   Gordon K Smyth
• [BioC] Separate Channel Analysis of Two-Color Data   Naomi Altman
• [BioC] Separate Channel Analysis of Two-Color Data   Gordon Smyth
• [BioC] Compare results from different analysis (Affymetrix)   Ingrid H. G. Østensen
• [BioC] Compare results from different analysis (Affymetrix)   Sean Davis
• [BioC] Compare results from different analysis (Affymetrix)   Ingrid H. G. Østensen
• [BioC] Compare results from different analysis (Affymetrix)   Naomi Altman
• [BioC] trouble hacking plotPCA   Jenny Drnevich
• [BioC] Compare results from different analysis (Affymetrix)   Darlene Goldstein
• [BioC] trouble hacking plotPCA   James W. MacDonald
• [BioC] ExpressionSet, fitPLM confusion   Georg Otto
• [BioC] ExpressionSet, fitPLM confusion   Wolfgang Huber
• [BioC] namespace and other developer tools   Naomi Altman
• [BioC] ExpressionSet, fitPLM confusion   James W. MacDonald
• [BioC] topTable vs decideTests   Ingrid H. G. Østensen
• [BioC] namespace and other developer tools   James W. MacDonald
• [BioC] grid package   yanju
• [BioC] namespace and other developer tools   Naomi Altman
• [BioC] namespace and other developer tools   Seth Falcon
• [BioC] trouble hacking plotPCA   Jenny Drnevich
• [BioC] trouble hacking plotPCA   Martin Morgan
• [BioC] Chromosome view of Nimblegen data   Rustici, Gabriella (NIH/NCI) [F]
• [BioC] difference between annotation   gregory voisin
• [BioC] Chromosome view of Nimblegen data   Sean Davis
• [BioC] ExpressionSet, fitPLM confusion   Henrik Bengtsson
• [BioC] GO 1.13.0   Weiyin Zhou
• [BioC] topTable vs decideTests   Morten Mattingsdal
• [BioC] EST´s mapped to a structural variation region   João Fadista
• [BioC] Chromosome view of Nimblegen data   J.delasHeras at ed.ac.uk
• [BioC] difference between annotation   Michal Okoniewski
• [BioC] converting GEO soft files to MS excel files   Sean Davis
• [BioC] EST´s mapped to a structural variation region   Sean Davis
• [BioC] difference between annotation   Maria Stalteri
• [BioC] CDF and Annotation-GeneChip Porcine Genome Array   Angeles Jiménez Marín
• [BioC] How to use a string as an environment name in mget?   Jarno Tuimala
• [BioC] How to use a string as an environment name in mget?   Wolfgang Huber
• [BioC] [Now off-topic] Chromosome view of Nimblegen data   Sean Davis
• [BioC] Chromosome view of Nimblegen data   James W. MacDonald
• [BioC] CDF and Annotation-GeneChip Porcine Genome Array   James W. MacDonald
• [BioC] What is a good method for analyzing differential expression from Illumina BeadStudio summary data?   Todd DeLuca
• [BioC] finding cliques with packages Graph and RBGL   Bagatti Davide
• [BioC] What is a good method for analyzing differential expression from Illumina BeadStudio summary data?   Kevin R. Coombes
• [BioC] number of digits to the right of the decimal point   D.Enrique ESCOBAR ESPINOZA
• [BioC] GO 1.13.0   Nianhua Li
• [BioC] number of digits to the right of the decimal point   James W. MacDonald
• [BioC] GO 1.13.0   Weiyin Zhou
• [BioC] affycoretools   Weiyin Zhou
• [BioC] affycoretools   James W. MacDonald
• [BioC] grid package   Herve Pages
• [BioC] affycoretools   Weiyin Zhou
• [BioC] EST´s mapped to a known structural variation region   João Fadista
• [BioC] Error in loess normalization   claudio.is at libero.it
• [BioC] Error in loess normalization   Wolfgang Huber
• [BioC] RMA question   James Anderson
• [BioC] RMA question   Wolfgang Huber
• [BioC] RMA question   Naomi Altman
• [BioC] finding cliques with packages Graph and RBGL   lilong at isb-sib.ch
• [BioC] RMA question   Dennis Kostka
• [BioC] RMA question   Harbron, Chris
• [BioC] linkage analysis   Theresa Scharl
• [BioC] linkage analysis   Sean Davis
• [BioC] RMA question   Lana Schaffer
• [BioC] How to read and normalize hundreds of CEL files?   Yair Benita
• [BioC] How to read and normalize hundreds of CEL files?   James W. MacDonald
• [BioC] How to read and normalize hundreds of CEL files?   Sean Davis
• [BioC] How to read and normalize hundreds of CEL files?   James Anderson
• [BioC] How to read and normalize hundreds of CEL files?   Jeff Gentry
• [BioC] affylmGUI problem with tkcmd   Wonjong Moon
• [BioC] affylmGUI problem with tkcmd   Seth Falcon
• [BioC] Illumina annotation packages   Lynn Amon
• [BioC] GOENTREZID2GO hard-coded in GOstats:makeGOGraph   Paul Shannon
• [BioC] "alt splice ANOVA like"   Malick.PAYE at eu.biomerieux.com
• [BioC] finding cliques with packages Graph and RBGL   Bagatti Davide
• [BioC] Problems with BioConductor 1.9 in R-2.4.1   Groot, Philip de
• [BioC] finding cliques with packages Graph and RBGL   lilong at isb-sib.ch
• [BioC] RMA Question   MPorter at genelogic.com
• [BioC] Where do I find the golub_Train dataset?   Benjamin Otto
• [BioC] Where do I find the golub_Train dataset?   Furge, Kyle
• [BioC] Where do I find the golub_Train dataset?   Seth Falcon
• [BioC] affylmGUI problem with tkcmd   Wonjong Moon
• [BioC] RODBC and odbcConnectExcel   Wolfgang Raffelsberger
• [BioC] finding cliques with packages Graph and RBGL   Bagatti Davide
• [BioC] Problems with BioConductor 1.9 in R-2.4.1   Seth Falcon
• [BioC] affycoretools   Weiyin Zhou
• [BioC] GOENTREZID2GO hard-coded in GOstats:makeGOGraph   Seth Falcon
• [BioC] BioC Advanced Course Jan 10th-12th (Space Still Available)   Seth Falcon
• [BioC] affycoretools   James W. MacDonald
• [BioC] confused about Mann-Whitney in MTP   Obi Griffith
• [BioC] affycoretools   Weiyin Zhou
• [BioC] affycoretools   James W. MacDonald
• [BioC] affycoretools   James W. MacDonald
• [BioC] affycoretools   Weiyin Zhou
• [BioC] affycoretools   Weiyin Zhou
• [BioC] affylmGUI problem with tkcmd   Keith Satterley
• [BioC] bioconductor   Kesavan Asaithambi
• [BioC] bioconductor   Seth Falcon
• [BioC] bioconductor   Kesavan Asaithambi
• [BioC] finding cliques with packages Graph and RBGL   lilong at isb-sib.ch
• [BioC] aCGH install requied sma   zhu zhidong
• [BioC] finding cliques with packages Graph and RBGL   Bagatti Davide
• [BioC] aCGH install requied sma   Seth Falcon
• [BioC] RODBC and odbcConnectExcel   James W. MacDonald
• [BioC] aCGH install requied sma   zhu zhidong
• [BioC] aCGH install requied sma   Seth Falcon
• [BioC] limma - MA   João Fadista
• [BioC] limma - MA   Hans-Ulrich Klein
• [BioC] HGU133 spike-in   Talloen, Willem [PRDBE]
• [BioC] Where do I find the golub_Train dataset?   Benjamin Otto
• [BioC] Where do I find the golub_Train dataset?   Kasper Daniel Hansen
• [BioC] Where do I find the golub_Train dataset?   Benjamin Otto
• [BioC] Where do I find the golub_Train dataset?   Furge, Kyle
• [BioC] Where do I find the golub_Train dataset?   Seth Falcon
• [BioC] limma - MA   Jenny Drnevich
• [BioC] subset of RG - limma   João Fadista
• [BioC] subset of RG - limma   michael watson (IAH-C)
• [BioC] Developer Meeting in Lausanne CH 4.+5. April 2007   Wolfgang Huber
• [BioC] problems when connecting to biomaRt database   Lina Hultin-Rosenberg
• [BioC] problems when connecting to biomaRt database   Wolfgang Huber
• [BioC] Plate or print-order effects - limma   João Fadista
• [BioC] AnnBuilder error: parseData can't access some tmp file   Benjamin Otto
• [BioC] merge two tables and filte......   Weiyin Zhou
• [BioC] merge two tables and filte......   Sean Davis
• [BioC] reference signal equal to 0   Yolande Tra
• [BioC] hyperG on custermized categories   Weiwei Shi
• [BioC] hyperG on custermized categories   Seth Falcon
• [BioC] Plate or print-order effects - limma   J.delasHeras at ed.ac.uk
• [BioC] problem with hist.default in affystart in package affycoretools   Kimpel, Mark William
• [BioC] problem with hist.default in affystart in package affycoretools   James W. MacDonald
• [BioC] problem with hist.default in affystart in package affycoretools   Kimpel, Mark William
• [BioC] AnnBuilder error: parseData can't access some tmp file   Nianhua Li
• [BioC] symbol to location   Rafael A Irizarry
• [BioC] symbol to location   Steffen Durinck
• [BioC] symbol to location   Rafael A Irizarry
• [BioC] Rgraphviz update for BioC 1.9   Kasper Daniel Hansen
• [BioC] (no subject)   Charlyn Suarez

Last message date: Sat Dec 30 02:42:15 CET 2006
Archived on: Tue Jan 2 17:44:44 CET 2007

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