June 2006 Archives by author

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Starting: Thu Jun 1 00:23:05 CEST 2006
Ending: Fri Jun 30 16:33:44 CEST 2006
Messages: 325

• [BioC] Limma, dye-swaps and uneven numbers of replicate arrays   michael watson (IAH-C)
• [BioC] biomaRt error and no devel package for windows?   michael watson (IAH-C)
• [BioC] just.gcrma and normalisation   alex lam (RI)
• [BioC] BioC2006 conference scholarship program, applications due 15 June 2006   Vincent Carey 525-2265
• [BioC] updated BioC2006 conference scholarship offerings   Vincent Carey 525-2265
• [BioC] possible boston bioconductor training, 13-15 july 2006   Vincent Carey 525-2265
• [BioC] registration materials for boston bioc training now available   Vincent Carey 525-2265
• [BioC] environment   Afsaneh
• [BioC] classifier using R   Naomi Altman
• [BioC] duplicateCorrelation and day effect in limma   Naomi Altman
• [BioC] qc and fitPLM functions in 'simpleaffy' and 'affyPLM'   Alvord, Greg (DMS) [Contr]
• [BioC] How to read a subset of the .CEL files   Alvord, Greg (DMS) [Contr]
• [BioC] How to read a subset of the .CEL files   Alvord, Greg (DMS) [Contr]
• [BioC] flat microarray p-values   Darren Ames
• [BioC] FW: flat microarray p-values   Darren Ames
• [BioC] flat microarray p-values   Darren Ames
• [BioC] flat microarray p-values   Darren Ames
• [BioC] invalid gpr characters?   Darren Ames
• [BioC] Duplicate row.names error   Andre
• [BioC] Combining two datasets - help to use GeneMeta.   Gordon Barr
• [BioC] limma: get all sig genes from multiple contrasts   Ivan Baxter
• [BioC] limma: get all sig genes from multiple contrasts   Ivan Baxter
• [BioC] hopach and heatmap   Ivan Baxter
• [BioC] spotsegmentation   Abdel Benajjou
• [BioC] multi PMT scan combination   Henrik Bengtsson
• [BioC] single-channel GenePix data   Henrik Bengtsson
• [BioC] How to read a subset of the .CEL files   Henrik Bengtsson
• [BioC] qc and fitPLM functions in 'simpleaffy' and 'affyPLM'   Ben Bolstad
• [BioC] median of the NUSE value   Ben Bolstad
• [BioC] just.gcrma and normalisation   Ben Bolstad
• [BioC] a problem with package limma (read.maimages)   Svetlana Bulashevska
• [BioC] single-channel GenePix data   Svetlana Bulashevska
• [BioC] RBGL1.8 on 64bit Linux?   Celine Carret
• [BioC] RBGL1.8 on 64bit Linux?   Celine Carret
• [BioC] [Fwd: Re: RBGL1.8 on 64bit Linux?]   Celine Carret
• [BioC] [Fwd: Re: RBGL1.8 on 64bit Linux?]   Celine Carret
• [BioC] query gramene from biomaRt package   Tine Casneuf
• [BioC] Reading flag data from Agilent files   Florian Chain
• [BioC] Two Slides Question   Chen, Kegui
• [BioC] Two Slides Question   Chen, Kegui
• [BioC] decideTests with nestedF   Ariel Chernomoretz
• [BioC] In silico interactomes   Tony Chiang
• [BioC] 2 Courses Near You - (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor, (2) R/Splus Fundamentals and Programming Techniques   Francois Collin
• [BioC] Reading flag data from Agilent files   Giovanni Coppola
• [BioC] multi PMT scan combination   Miroslava Cuperlovic-Culf
• [BioC] II Atlantic Microarray Symposium, August 24-25, Moncton NB, Canada   Miroslava Cuperlovic-Culf
• [BioC] limma: duplicateCorrelation   Christelle Dantec
• [BioC] "M vs. M" Plot   Sean Davis
• [BioC] flat microarray p-values   Sean Davis
• [BioC] Fwd: Problem with justRMA and hgu133aplus2cdf   Sean Davis
• [BioC] [Bioc-devel] Appropriate linear model analysis for microarray time course comparison   Sean Davis
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   Sean Davis
• [BioC] Combining two datasets - help to use GeneMeta.   Sean Davis
• [BioC] Scripts to handle array CGH data files from NimbleGen   Sean Davis
• [BioC] decideTests with nestedF   Sean Davis
• [BioC] single-channel GenePix data   Sean Davis
• [BioC] affy & problems with memory   Yi-Mo Deng
• [BioC] problem with biomaRt and mouse affy queries   Vincent Detours
• [BioC] VennDiagram quesiont in limma   Jenny Drnevich
• [BioC] VennDiagram quesiont in limma - mistake correction   Jenny Drnevich
• [BioC] RMA-bimodality:   Jenny Drnevich
• [BioC] unnormalised vs normalised distribution   Jenny Drnevich
• [BioC] plotAffyRNAdeg x-axis length of RNA digestion plot   Jenny Drnevich
• [BioC] How to read a subset of the .CEL files   Jenny Drnevich
• [BioC] LimmaGUI for illumina data   Mark Dunning
• [BioC] problem with biomaRt and mouse affy queries   Steffen Durinck
• [BioC] combined Affybatch and mas5   Lewin Eisele
• [BioC] error message in gcrma   Mohammad Esad-Djou
• [BioC] error message in gcrma   Mohammad Esad-Djou
• [BioC] error message in gcrma   Mohammad Esad-Djou
• [BioC] error message in gcrma   Mohammad Esad-Djou
• [BioC] Package wyr?   Mohammad Esad-Djou
• [BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs   Seth Falcon
• [BioC] Issue with removeNode?   Seth Falcon
• [BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs (fwd)   Seth Falcon
• [BioC] Rmpi installation in in IBM HCP   Seth Falcon
• [BioC] R hangs when applying johnson.all.pairs.sp (in library RBGL) to some graphs   Seth Falcon
• [BioC] Update getBioC for R 2.3 needed ?   Seth Falcon
• [BioC] problem with moe430a version 1.12.0?   Seth Falcon
• [BioC] Issue with removeNode?   Seth Falcon
• [BioC] Issue with removeNode?   Seth Falcon
• [BioC] Problem downloading Bioconductor   Seth Falcon
• [BioC] Problems with installation of Rgraphviz   Seth Falcon
• [BioC] error message in gcrma   Seth Falcon
• [BioC] error message in gcrma   Seth Falcon
• [BioC] error message in gcrma   Seth Falcon
• [BioC] R hangs when applying johnson.all.pairs.sp (in library RBGL) to some graphs   Seth Falcon
• [BioC] error message in gcrma   Seth Falcon
• [BioC] help with large Rgraphviz output   Seth Falcon
• [BioC] help with large Rgraphviz output   Seth Falcon
• [BioC] problem with latest version of graph   Seth Falcon
• [BioC] BioC2006 Conference, Aug 3-4 in Seattle   Seth Falcon
• [BioC] [SPAM] Re: Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   Seth Falcon
• [BioC] R warning: no package 'temp' was found   Seth Falcon
• [BioC] Rgraphviz edge weight question   Seth Falcon
• [BioC] Ruuid had non-zero exit status   Seth Falcon
• [BioC] Ruuid had non-zero exit status   Seth Falcon
• [BioC] Rgraphviz edge weight question   Seth Falcon
• [BioC] Question about the appropriate uniververse for GOHyperG or hyperGtable   Seth Falcon
• [BioC] error creating new exprSet   Seth Falcon
• [BioC] Problems loading biomaRt and XML   Seth Falcon
• [BioC] Problems loading biomaRt and XML   Seth Falcon
• [BioC] Copying text from www.bioconductor.org web pages?   Seth Falcon
• [BioC] Combining two datasets - help to use GeneMeta.   Robert Gentleman
• [BioC] Combining two datasets - help to use GeneMeta.   Robert Gentleman
• [BioC] Ruuid had non-zero exit status   Robert Gentleman
• [BioC] Question about the appropriate uniververse for GOHyperG or hyperGtable   Robert Gentleman
• [BioC] environment   Thomas Girke
• [BioC] vector allocation error   Thomas Girke
• [BioC] Copying text from www.bioconductor.org web pages?   Earl F. Glynn
• [BioC] Combining two datasets - help to use GeneMeta.   Darlene Goldstein
• [BioC] vsn and RMA-affy ...?   Dario Greco
• [BioC] AnnBuilder problem.   Dario Greco
• [BioC] getBM failing on complete probe list for hgu133plus2   Obi Griffith
• [BioC] empty elements in uniprot_swissprot annotation   Obi Griffith
• [BioC] One channel microarray antibody analysis   Jordi Altirriba Gutiérrez
• [BioC] Problems loading biomaRt and XML   Jordi Altirriba Gutiérrez
• [BioC] Problems loading biomaRt and XML   Jordi Altirriba Gutiérrez
• [BioC] Imaging of Protein Array   Jordi Altirriba Gutiérrez
• [BioC] error message in gcrma   Kasper Daniel Hansen
• [BioC] Can't find survival and splines packages - help?   Kasper Daniel Hansen
• [BioC] [Spam:8.0] Re: R command history on unix version   Kasper Daniel Hansen
• [BioC] understanding of makeContrats() in Limma   Stephen Henderson
• [BioC] environment   Stephen Henderson
• [BioC] classifier using R   Stephen Henderson
• [BioC] marray: removing flagged spots from loess normalization   Oliver R. Homann
• [BioC] getBM failing on complete probe list for hgu133plus2   Wolfgang Huber
• [BioC] vsn on log2 transformed data?   Wolfgang Huber
• [BioC] vsn and RMA-affy ...?   Wolfgang Huber
• [BioC] RMA-bimodality:   Wolfgang Huber
• [BioC] RMA-bimodality:   Wolfgang Huber
• [BioC] RMA-bimodality:   Wolfgang Huber
• [BioC] RMA-bimodality:   Wolfgang Huber
• [BioC] Developers Day 2. Aug 2006   Wolfgang Huber
• [BioC] Rgraphviz edge weight question   Wolfgang Huber
• [BioC] Scripts to handle array CGH data files from NimbleGen   Wolfgang Huber
• [BioC] multtest error - class label problem   Wolfgang Huber
• [BioC] problem with biomaRt and mouse affy queries   Wolfgang Huber
• [BioC] less mappings to LocusLink in new moe430a   Manuela Hummel
• [BioC] help with large Rgraphviz output   Jake
• [BioC] Rmpi loading error --- updates   Jake
• [BioC] VennDiagram quesiont in limma   Jianping Jin
• [BioC] R command history on unix version   Jianping Jin
• [BioC] [Spam:8.0] Re: R command history on unix version   Jianping Jin
• [BioC] [Spam:8.0] Re: [Spam:8.0] Re: R command history on unix version   Jianping Jin
• [BioC] plotAffyRNAdeg x-axis length of RNA digestion plot   Sue Jones
• [BioC] limma : design matrix and topTable M values   Sue Jones
• [BioC] query gramene from biomaRt package   Arek Kasprzyk
• [BioC] limma duplicateCorrelation does not return 'all.correlations'   Krys Kelly
• [BioC] help with large Rgraphviz output   Kimpel, Mark William
• [BioC] help with large Rgraphviz output   Kimpel, Mark William
• [BioC] problem with latest version of graph   Kimpel, Mark William
• [BioC] problem with latest version of graph   Kimpel, Mark William
• [BioC] Rgraphviz edge weight question   Kimpel, Mark William
• [BioC] Rgraphviz edge weight question   Kimpel, Mark William
• [BioC] Rgraphviz edge weight question   Kimpel, Mark William
• [BioC] rflowcyt and prada questions   Nolwenn LeMeur
• [BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs (fwd)   Nolwenn LeMeur
• [BioC] Research Associate Positions in Statistical Bioinformatics   Jae K. Lee
• [BioC] less mappings to LocusLink in new moe430a   Nianhua Li
• [BioC] environment   Nianhua Li
• [BioC] mouse4302   Nianhua Li
• [BioC] AnnBuilder problem.   Nianhua Li
• [BioC] justGCRMA error in BioC 1.8   James W. MacDonald
• [BioC] limma: results from different coefficients   James W. MacDonald
• [BioC] vsn on log2 transformed data?   James W. MacDonald
• [BioC] Error in SSClust (Smoothing Spline Clustering)   James W. MacDonald
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   James W. MacDonald
• [BioC] Creating a Custom CDF Environment   James W. MacDonald
• [BioC] limma: get all sig genes from multiple contrasts   James W. MacDonald
• [BioC] limma: get all sig genes from multiple contrasts   James W. MacDonald
• [BioC] biomaRt error and no devel package for windows?   James W. MacDonald
• [BioC] R command history on unix version   James W. MacDonald
• [BioC] Question about the appropriate uniververse for GOHyperG or hyperGtable   James W. MacDonald
• [BioC] plotAffyRNAdeg x-axis length of RNA digestion plot   James W. MacDonald
• [BioC] plotAffyRNAdeg x-axis length of RNA digestion plot   James W. MacDonald
• [BioC] [Spam:8.0] Re: R command history on unix version   James W. MacDonald
• [BioC] decideTests with nestedF   James W. MacDonald
• [BioC] decideTests with nestedF   James W. MacDonald
• [BioC] decideTests with nestedF   James W. MacDonald
• [BioC] How to read a subset of the .CEL files   James W. MacDonald
• [BioC] classifier using R   James W. MacDonald
• [BioC] limma output   James W. MacDonald
• [BioC] Where can I get cdf? was(affy & problems with memory)   James W. MacDonald
• [BioC] RMA-bimodality:   Claus Mayer
• [BioC] RMA-bimodality:   Claus Mayer
• [BioC] scripts to process array CGH data files from NimbleGen   Steven McKinney
• [BioC] Scripts to handle array CGH data files from NimbleGen   Steven McKinney
• [BioC] Copying text from www.bioconductor.org web pages?   Steven McKinney
• [BioC] Error in SSClust (Smoothing Spline Clustering)   Maurice Melancon
• [BioC] yeast2 LOCUSID environment   Jacob Michaelson
• [BioC] Imaging of Protein Array   Saroj Mohapatra
• [BioC] Imaging of Protein Array   Saroj Mohapatra
• [BioC] Copying text from www.bioconductor.org web pages?   Saroj Mohapatra
• [BioC] error creating new exprSet   Martin Morgan
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   Martin Morgan
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   Martin Morgan
• [BioC] xval in MLInterfaces package   Martin Morgan
• [BioC] xval in MLInterfaces package   Martin Morgan
• [BioC] classifier using R   Nadege Nana
• [BioC] vsn on log2 transformed data?   Kamila Naxerova
• [BioC] RNA deg correction?   Tarun Nayar
• [BioC] Simpleaffy QC error with Vinis vinifera chips   Tarun Nayar
• [BioC] A question regardin duplicate correlations in limma   Manish Neupane
• [BioC] multtest error - class label problem   Yuhong Ning
• [BioC] "M vs. M" Plot   Heather Nyce
• [BioC] Question about the appropriate uniververse for GOHyperG or hyperGtable   Ochsner, Scott A
• [BioC] unnormalised vs normalised distribution   Michal Okoniewski
• [BioC] Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1   Michael Oldham
• [BioC] Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1   Michael Oldham
• [BioC] Welch approximation: Degrees of freedom impact on pvalues   Benjamin Otto
• [BioC] W: unnormalised vs normalised distribution   Benjamin Otto
• [BioC] Ruuid had non-zero exit status   Herve Pages
• [BioC] Ruuid had non-zero exit status   Herve Pages
• [BioC] bioconductor.org down on Tuesday June 20th 2:00pm-2:10pm Pacific Time   Herve Pages
• [BioC] vector allocation error   Francois Pepin
• [BioC] error creating new exprSet   Peter
• [BioC] vector allocation error   Ulrich Pfeffer
• [BioC] multtest error - class label problem   Katherine Pollard
• [BioC] decideTest extraction of P values   Vijay A Raghavan
• [BioC] Scripts to handle array CGH data files from NimbleGen   Todd Richmond
• [BioC] How to read a subset of the .CEL files   Roayaei, Jean (DMS) [Contr]
• [BioC] blocking in limma gives an estimability problem   Pedro López Romero
• [BioC] paired samples and duplicateCorrelation iin limma   Pedro López Romero
• [BioC] decideTests with nestedF   Pedro López Romero
• [BioC] decideTests with nestedF   Pedro López Romero
• [BioC] decideTests with nestedF   Pedro López Romero
• [BioC] decideTests with nestedF   Pedro López Romero
• [BioC] decideTests with nestedF   Pedro López Romero
• [BioC] duplicateCorrelation and day effect in limma   Pedro López Romero
• [BioC] The ECCB early-registration deadline is July 10th!   Hershel Safer
• [BioC] A question regardin duplicate correlations in limma   Keith Satterley
• [BioC] rbind of MALists   Matthew Scholz
• [BioC] rbind of MALists   Matthew Scholz
• [BioC] multi PMT scan combination   Matthew Scholz
• [BioC] Can't find survival and splines packages - help?   Fernanda Schreiber
• [BioC] Problems with installing packages   David Seo
• [BioC] annotation data packages for plasmodium falciparum?   Paul Shannon
• [BioC] Combining two datasets - help to use GeneMeta.   Sharon
• [BioC] Combining two datasets - help to use GeneMeta.   Sharon
• [BioC] guidance for making appropriate design matrix - for limmma use   Sharon
• [BioC] Error in using qc in simpleaffy.   Sharon
• [BioC] problem with limma and BlueFuse   M L Smith
• [BioC] Limma contrasts questions   Gordon Smyth
• [BioC] VennDiagram quesiont in limma   Gordon Smyth
• [BioC] limma citations [was LimmaGUI for illumina data]   Gordon Smyth
• [BioC] rbind of MALists   Gordon Smyth
• [BioC] decideTests with nestedF   Gordon Smyth
• [BioC] a problem with package limma (read.maimages)   Gordon Smyth
• [BioC] limma duplicateCorrelation does not return 'all.correlations'   Gordon Smyth
• [BioC] limma decideTests   Gordon K Smyth
• [BioC] Limma, dye-swaps and uneven numbers of replicate arrays   Gordon K Smyth
• [BioC] question on decideTests function in limma   Gordon K Smyth
• [BioC] decideTest extraction of P values   Gordon K Smyth
• [BioC] Subsetting limma TestResults   Gordon K Smyth
• [BioC] rbind of MALists   Gordon K Smyth
• [BioC] rbind of MALists   Gordon K Smyth
• [BioC] limma: duplicateCorrelation   Gordon K Smyth
• [BioC] log2 ratio as limma input   Gordon K Smyth
• [BioC] problem with limma and BlueFuse   Gordon K Smyth
• [BioC] query gramene from biomaRt package   Will Spooner
• [BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs   Ulrik Stervbo
• [BioC] Subsetting limma TestResults   Michael Strehle
• [BioC] Issue with removeNode?   Jonathan Swinton
• [BioC] simpleaffy package: Exporting a PairComp object   Suzanne Szak
• [BioC] Positions in Biostatistics/Bioinformatics   Therese Sørlie
• [BioC] goCluster results   TM
• [BioC] goCluster colors   TM
• [BioC] display goCluster graph with specific go term   TM
• [BioC] goCluster plot interpretation   TM
• [BioC] goCluster plot with heatmap visualization method   TM
• [BioC] multiple comparisons   Tarca, Adi
• [BioC] 2 Courses Near You - (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor, (2) R/Splus Fundamentals and Programming Techniques   Sue Turner
• [BioC] problem with limma and BlueFuse   Alessio Venier
• [BioC] vsn and microarray blank spots   Alessio Venier
• [BioC] BIRD   Prof.Roland Wagner
• [BioC] RMA-bimodality:   Peter G. Warren
• [BioC] RMA-bimodality:   Peter G. Warren
• [BioC] RMA-bimodality:   Peter G. Warren
• [BioC] Mouse exon array probes   Richard Williams
• [BioC] Differential expression   Di Wu
• [BioC] xval in MLInterfaces package   Wu, Xiwei
• [BioC] xval in MLInterfaces package   Wu, Xiwei
• [BioC] just.gcrma and normalisation   Zhijin (Jean) Wu
• [BioC] Duplicate row.names error   Jean Yee Hwa Yang
• [BioC] Rmpi loading error   Ye, Bin
• [BioC] Rmpi loading error --- updates   Ye, Bin
• [BioC] Rmpi loading error --- updates   Ye, Bin
• [BioC] R warning: no package 'temp' was found   Zhang, Jacob
• [BioC] yeast2 LOCUSID environment   John Zhang
• [BioC] environment   John Zhang
• [BioC] RMA-bimodality:   Phguardiol at aol.com
• [BioC] Farms library   phguardiol at aol.com
• [BioC] unnormalised vs normalised distribution   botto
• [BioC] In silico interactomes   maria at cbm.bio.uniroma2.it
• [BioC] Creating a Custom CDF Environment   martin doherty
• [BioC] Background correlation with different scanners   J.delasHeras at ed.ac.uk
• [BioC] day-of-hybridisation variability   kfbargad at ehu.es
• [BioC] error creating new exprSet   kfbargad at ehu.es
• [BioC] limma: get all sig genes from multiple contrasts   kfbargad at ehu.es
• [BioC] median of the NUSE value   kfbargad at ehu.es
• [BioC] median of the NUSE value   kfbargad at ehu.es
• [BioC] VennDiagram quesiont in limma   jjin at email.unc.edu
• [BioC] Ruuid had non-zero exit status   zph at herald.ox.ac.uk
• [BioC] Ruuid had non-zero exit status   zph at herald.ox.ac.uk
• [BioC] Ruuid had non-zero exit status   zph at herald.ox.ac.uk
• [BioC] Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1   zph at herald.ox.ac.uk
• [BioC] Ruuid had non-zero exit status   zph at herald.ox.ac.uk
• [BioC] R hangs when applying johnson.all.pairs.sp (in library RBGL) to some graphs   Li.Long at isb-sib.ch
• [BioC] RBGL1.8 on 64bit Linux?   Li.Long at isb-sib.ch
• [BioC] RBGL1.8 on 64bit Linux?   Li.Long at isb-sib.ch
• [BioC] [Fwd: Re: RBGL1.8 on 64bit Linux?]   Li.Long at isb-sib.ch
• [BioC] log2 ratio as limma input   yuhong ning
• [BioC] multtest error - class label problem   yuhong ning
• [BioC] day-of-hybridisation variability   martin.schumacher at novartis.com
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   rcaloger
• [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   rcaloger
• [BioC] [SPAM] Re: Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7   rcaloger
• [BioC] RMA-bimodality:   noel0925 at sbcglobal.net
• [BioC] RMA-bimodality:   noel0925 at sbcglobal.net
• [BioC] query gramene from biomaRt package   sdurinck
• [BioC] normalize.AffyBatch.quantiles and NA values   odlc at uchicago.edu
• [BioC] understanding of makeContrats() in Limma   gregory voisin
• [BioC] limma output   stephanie walter
• [BioC] Imaging of Protein Array   内田靖哉

Last message date: Fri Jun 30 16:33:44 CEST 2006
Archived on: Sat Jul 1 09:05:45 CEST 2006

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• More info on this list...