October 2007 Archives by author

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Starting: Mon Oct 1 14:54:46 CEST 2007
Ending: Wed Oct 31 23:59:29 CET 2007
Messages: 496

• [BioC] limmaGUI and Agilent output files!   "Gras Peña, Rafael"
• [BioC] Bead Array   Divinya Abraham
• [BioC] Arabidopsis GO Pie Charts   Naomi Altman
• [BioC] Arabidopsis GO Pie Charts   Naomi Altman
• [BioC] limma - paired design   Naomi Altman
• [BioC] limma - paired design   Naomi Altman
• [BioC] illumina annotation package error   Lynn Amon
• [BioC] illumina annotation package error   Lynn Amon
• [BioC] Illumina annotation packages   Lynn Amon
• [BioC] are older versions of Ensembl accessible with biomaRt?   Lynn Amon
• [BioC] warning message in KS test   James Anderson
• [BioC] warning message in KS test   James Anderson
• [BioC] warning message in KS test   James Anderson
• [BioC] warning message in KS test   James Anderson
• [BioC] question regarding .632plus error rate estimator in ipred package   James Anderson
• [BioC] brb arraytools and excel 2007   Dr Gyorffy Balazs
• [BioC] BACKGROUND CORRECTION AND NORMALIZATION FOR VERY SMALL CUSTOMIZED ARRAYS   Bandyopadhyay, Somnath (Som)
• [BioC] package for human ST gene arrays?   Yongde Bao
• [BioC] package for human ST gene arrays?   Yongde Bao
• [BioC] Is a number within a set of ranges?   Carlos J. Gil Bellosta
• [BioC] CEL files with different size   Henrik Bengtsson
• [BioC] reading many affy U133 Plus_2.0   Henrik Bengtsson
• [BioC] running time of snapCGH processCGH and runDNAcopy   Henrik Bengtsson
• [BioC] affxparser fails to convert AGCC format cel file   Henrik Bengtsson
• [BioC] affxparser fails to convert AGCC format cel file   Henrik Bengtsson
• [BioC] package for human ST gene arrays?   Henrik Bengtsson
• [BioC] eQTL postdoc position   Dave Berger
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for   Dick Beyer
• [BioC] suppress messages in rma   Ben Bolstad
• [BioC] Your Open Access Paper   Phil Bourne
• [BioC] Is a number within a set of ranges?   Daniel Brewer
• [BioC] Is a number within a set of ranges?   Daniel Brewer
• [BioC] Limma: eBayes makes p-values larger   Daniel Brewer
• [BioC] retrieving SNP names for MM probes using oligo   Stacey Burrows
• [BioC] AnnBuilder: problem with kegg url?   Marc Carlson
• [BioC] GO classification   Marc Carlson
• [BioC] GOstats install error under Linux Debian   Marc Carlson
• [BioC] Annotation package for Yeast Genome S98 array ?   Marc Carlson
• [BioC] YGS98 package does not provide locus link ID information ?   Marc Carlson
• [BioC] markersymol filter problem   Marc Carlson
• [BioC] GO classification   Celine Carret
• [BioC] Making a PD package for Oligo   Benilton Carvalho
• [BioC] Normalization with a reference sample   Benilton Carvalho
• [BioC] rma data retrieve   Benilton Carvalho
• [BioC] retrieving SNP names for MM probes using oligo   Benilton Carvalho
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Carvalho, Benilton
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Benilton Carvalho
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Benilton Carvalho
• [BioC] error with affyPLM   Tony Chiang
• [BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"   Tony Chiang
• [BioC] GOStats/RBGL installation error   Tony Chiang
• [BioC] CAMDA07 publishing in Genomics   Ana Conesa
• [BioC] maSigPro questions   Ana Conesa
• [BioC] CAMDA 2007 Conference: EMERALD Worshop and student fellowships available. Poster submission deadline extended.   Ana Conesa
• [BioC] CAMDA 2007 Conference: Paper submission deadline extended.   Ana Conesa
• [BioC] maSigPro questions   Ana Conesa
• [BioC] How to create nested data frames   Ana Conesa
• [BioC] How to create nested data frames   Ana Conesa
• [BioC] heatmap_plus and distances   Aedin Culhane
• [BioC] All 3' UTRs for an organism - biomaRt package   Urska Cvek
• [BioC] Microarray data with outliers   JUAN MIGUEL MARIN DIAZARAQUE
• [BioC] Chromosome 23 and 24 dropped after run snapCGH processCGH   Sean Davis
• [BioC] brb arraytools and excel 2007   Sean Davis
• [BioC] Agilent 4x44 single color expression arrays   Sean Davis
• [BioC] running time of snapCGH processCGH and runDNAcopy   Sean Davis
• [BioC] running time of snapCGH processCGH and runDNAcopy   Sean Davis
• [BioC] snapCGH: log2ratio   Sean Davis
• [BioC] segmentation aCGH data   Sean Davis
• [BioC] segmentation aCGH data   Sean Davis
• [BioC] segmentation aCGH data   Sean Davis
• [BioC] heatmap_plus and distances   Sean Davis
• [BioC] heatmap_plus and distances   Sean Davis
• [BioC] Illumina replicates - packages   Sean Davis
• [BioC] About between-array normalization in limma   Sean Davis
• [BioC] 2 Test Samples on 1 Array   Sean Davis
• [BioC] Illumina annotation packages   Sean Davis
• [BioC] Microarray data with outliers   Sean Davis
• [BioC] Is a number within a set of ranges?   Sean Davis
• [BioC] print layout for Agilent data?   Sean Davis
• [BioC] print layout for Agilent data?   Sean Davis
• [BioC] print layout for Agilent data?   Sean Davis
• [BioC] topTable threshold on p-value and logFC [Re: was design matrix]   Marcus Davy
• [BioC] topTable threshold on p-value and logFC [Re: was design matrix]   Marcus Davy
• [BioC] topTable threshold on p-value and logFC [Re: was design matrix]   Marcus Davy
• [BioC] About between-array normalization in limma   De-Jian,ZHAO
• [BioC] About the three weights in limma   De-Jian,ZHAO
• [BioC] limma eBayes() produces NA in fit$F.p.value   De-Jian,ZHAO
• [BioC] when to impute the missing value?   De-Jian,ZHAO
• [BioC] segmentation aCGH data   Ramon Diaz-Uriarte
• [BioC] segmentation aCGH data   Ramon Diaz-Uriarte
• [BioC] About between-array normalization in limma   Ramon Diaz-Uriarte
• [BioC] Human whole genome Codelink arrays and paired analysis   Diego Diez
• [BioC] Making a PD package for Oligo   Colleen Doherty
• [BioC] Making a PD package for Oligo   Colleen Doherty
• [BioC] Making a PD package for Oligo   Colleen Doherty
• [BioC] lmFit and topTable   Jenny Drnevich
• [BioC] HELP! lmFit and duplicateCorrelation   Jenny Drnevich
• [BioC] HELP! lmFit and duplicateCorrelation   Jenny Drnevich
• [BioC] HELP! lmFit and duplicateCorrelation   Jenny Drnevich
• [BioC] HELP! lmFit and duplicateCorrelation   Jenny Drnevich
• [BioC] HELP! lmFit and duplicateCorrelation   Jenny Drnevich
• [BioC] lumi: LumiBatch slots don't match documentation   Pan Du
• [BioC] lumi: how is the controlData to be read and used?   Pan Du
• [BioC] lumi: how is the controlData to be read and used?   Pan Du
• [BioC] lumi: how is the controlData to be read and used?   Pan Du
• [BioC] ABarray package in R 2.6.0: error message   Vanessa Dumeaux
• [BioC] GO classification   Steffen Durinck
• [BioC] are older versions of Ensembl accessible with biomaRt?   Steffen Durinck
• [BioC] getGene type not recognized   Steffen Durinck
• [BioC] simple biomaRt query   Heidi Dvinge
• [BioC] Microarray bioinformatics position announcement - CRG - Barcelona, Spain   Lauro Sumoy Van Dyck
• [BioC] limma - paired design   Mayra Eduardoff
• [BioC] limma - paired design   Mayra Eduardoff
• [BioC] limma block design   Mayra Eduardoff
• [BioC] Viel Erfolg im top Ka.s_i_no...   Efren
• [BioC] Limma: Normalization with large numbers of differentially expressed genes   Serge Eifes
• [BioC] RE : Limma: Normalization with large numbers ofdifferentially expressed genes   Serge Eifes
• [BioC] RE : RE : Limma: Normalization with largenumbers ofdifferentially expressed genes   Serge Eifes
• [BioC] newbie Q about object identity   Thomas Elliott
• [BioC] KEGG & hyperGTest: an example?   Seth Falcon
• [BioC] Errors in importing cel files into oneChannelGUI   Ester Feldmesser
• [BioC] print layout for Agilent data?   John Fernandes
• [BioC] Affymetrix quality control metrics with simpleaffy   Richard Friedman
• [BioC] R crashes after image array plots hgu133plus2 in R2.6.0   Richard Friedman
• [BioC] R crashes after image array plots hgu133plus2 in R2.6.0   Richard Friedman
• [BioC] R crashes after image array plots hgu133plus2 in R2.6.0   Richard Friedman
• [BioC] AnnBuilder: problem with kegg url?   Matthias E. Futschik
• [BioC] GO classification   Ganiraju
• [BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"   Robert Gentleman
• [BioC] Download problem   Robert Gentleman
• [BioC] KEGG & hyperGTest: an example?   Robert Gentleman
• [BioC] Short Course in Seattle   Robert Gentleman
• [BioC] GOStats/RBGL installation error   Robert Gentleman
• [BioC] GSEAbase example? [was KEGG & hyperGTest: an example?]   Robert Gentleman
• [BioC] OntoCompare Error   Sebastien Gerega
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Thomas Girke
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Thomas Girke
• [BioC] GOstats install error under Linux Debian   Thomas Girke
• [BioC] GOstats install error under Linux Debian   Thomas Girke
• [BioC] GO classification   Thomas Girke
• [BioC] GO classification   Thomas Girke
• [BioC] Bioinformatic Faculty Position   Thomas Girke
• [BioC] Plotting question: how to plot SNP location data?   Thomas Girke
• [BioC] sequence search using a position weight matrix?   Paul Gordon
• [BioC] biocLite() and getBioC scripts install development packages!   Groot, Philip de
• [BioC] biocLite() and getBioC scripts install development packages!   Groot, Philip de
• [BioC] request for simple usage of probe level normalisations   Kasper Daniel Hansen
• [BioC] microRNA microarray analysis   Kasper Daniel Hansen
• [BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"   Kasper Daniel Hansen
• [BioC] package for human ST gene arrays?   Kasper Daniel Hansen
• [BioC] Expression levels of individual affymetrix probes   Kasper Daniel Hansen
• [BioC] combining data from two R arrays   Richard Harrison
• [BioC] combining data from two R arrays   Richard Harrison
• [BioC] Is a number within a set of ranges?   Christos Hatzis
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Liqun He
• [BioC] Plot Venn diagram for 5 sets   Liqun He
• [BioC] Programming   Courtney Heard
• [BioC] Bio/Chemoinformatics positions for OpenTox and Sens-it-iv projects   Christoph Helma
• [BioC] modify CDF file for array study   Hooiveld, Guido
• [BioC] predict vsn with reference   Wolfgang Huber
• [BioC] vsn and scaling   Wolfgang Huber
• [BioC] VSN: narrowing down probe sets for parameter estimation   Wolfgang Huber
• [BioC] VSN, RMA, dCHIP, etc....   Wolfgang Huber
• [BioC] Installing BioC + R 2.6: warnings   Paolo Innocenti
• [BioC] postdoc opportunities   Rafael Irizarry
• [BioC] HELP! lmFit and duplicateCorrelation   Al Ivens
• [BioC] rma data retrieve   Jianping Jin
• [BioC] rma data retrieve   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] print layout for Agilent data?   Jianping Jin
• [BioC] About beadarray package   Johnstone, Alice
• [BioC] About beadarray package   Johnstone, Alice
• [BioC] About beadarray package   Johnstone, Alice
• [BioC] BeadExplorer error   Johnstone, Alice
• [BioC] BeadExplorer error   Johnstone, Alice
• [BioC] Expression levels of individual affymetrix probes   Johnstone, Alice
• [BioC] Effect size and combined data sets   Andrej Kastrin
• [BioC] microRNA microarray analysis   Narendra Kaushik
• [BioC] Time-point analysis   Narendra Kaushik
• [BioC] beadarray - bead level image plots   Krys Kelly
• [BioC] ABarray   Sabah Khalid
• [BioC] contrasts in limma and missing values   Hans-Ulrich Klein
• [BioC] heatmap_plus and distances   Matthias Kohl
• [BioC] question regarding .632plus error rate estimator in ipredpackage   Kuhn, Max
• [BioC] Problems with k-cliq definition and calculations using RBGL package   Chanchal Kumar
• [BioC] Illumina annotation packages   Asta Laiho
• [BioC] heatmap_plus and distances   John Lande
• [BioC] getGene type not recognized   John Lande
• [BioC] getGene type not recognized   John Lande
• [BioC] CfP: Hackathon on Comparative Methods in R   Hilmar Lapp
• [BioC] Announcement: Software developer training for Galaxy, Tuesday, October 23 4:00pm - 6:00pm, San Diego (just before the ASHG meeting)   Ross Lazarus
• [BioC] annaffy - saveHTML changed behaviour in newer versions   Paul Leo
• [BioC] annaffy - saveHTML changed behaviour in newer versions   Paul Leo
• [BioC] annaffy - saveHTML changed behaviour in newer versions   Paul Leo
• [BioC] A question related to converting p values to -log p   Li, Aiguo (NIH/NCI) [C]
• [BioC] limma for R 2.6   Tiandao Li
• [BioC] limma for R 2.6   Tiandao Li
• [BioC] limma for R 2.6   Tiandao Li
• [BioC] lmFit and topTable   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] HELP! lmFit and duplicateCorrelation   Tiandao Li
• [BioC] residuals.MArrayLM   Tiandao Li
• [BioC] residuals.MArrayLM   Tiandao Li
• [BioC] residuals.MArrayLM   Tiandao Li
• [BioC] About between-array normalization in limma   Simon Lin
• [BioC] rule of MM design on Affymetrix?   Simon Lin
• [BioC] probelm of column names when using biomaRt   Li Lingdu
• [BioC] design matrix   James MacDonald
• [BioC] u133aaofav2   James MacDonald
• [BioC] design matrix   James W. MacDonald
• [BioC] adapt exprSet class   James W. MacDonald
• [BioC] Making a PD package for Oligo   James W. MacDonald
• [BioC] Making a PD package for Oligo   James W. MacDonald
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   James W. MacDonald
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   James W. MacDonald
• [BioC] GOstats - defining the gene universe   James W. MacDonald
• [BioC] reading many affy U133 Plus_2.0   James W. MacDonald
• [BioC] biocLite() and getBioC scripts install development packages!   James W. MacDonald
• [BioC] newbie Q about object identity   James W. MacDonald
• [BioC] A question related to converting p values to -log p   James W. MacDonald
• [BioC] u133aaofav2   James W. MacDonald
• [BioC] YGS98 package does not provide locus link ID information ?   James W. MacDonald
• [BioC] hugene10stv1probe?   James W. MacDonald
• [BioC] QC Parameter File error   James W. MacDonald
• [BioC] AMDA Update   James W. MacDonald
• [BioC] limma2biomaRt error   James W. MacDonald
• [BioC] rule of MM design on Affymetrix?   James W. MacDonald
• [BioC] Extracting data sub set from loaded data.   James W. MacDonald
• [BioC] getGene type not recognized   James W. MacDonald
• [BioC] How to create nested data frames   James W. MacDonald
• [BioC] package for human ST gene arrays?   James W. MacDonald
• [BioC] Expression levels of individual affymetrix probes   James W. MacDonald
• [BioC] Is a number within a set of ranges?   James W. MacDonald
• [BioC] Is a number within a set of ranges?   James W. MacDonald
• [BioC] Is a number within a set of ranges?   James W. MacDonald
• [BioC] Limma: eBayes makes p-values larger   James W. MacDonald
• [BioC] markersymol filter problem   Siarhei Manakou
• [BioC] markersymol filter problem   Siarhei Manakou
• [BioC] Certain student loans eradicated   Marilyn
• [BioC] Chromosome 23 and 24 dropped after run snapCGH processCGH   J-C. Marioni
• [BioC] processCGH in snapCGH package   J-C. Marioni
• [BioC] BSgenome.Mmusculus.UCSC.mm8 and BSgenome   Florian Markowetz
• [BioC] A question related to converting p values to -log p   Morten Mattingsdal
• [BioC] GOstats - defining the gene universe   Rachael McBride
• [BioC] GOstats - defining the gene universe   Rachael McBride
• [BioC] Problem reading data with beadarray package   Elizabeth McClellan
• [BioC] simpleaffy 2.14.02, setQCEnvironment   Crispin Miller
• [BioC] Problems with the spot quality weight with limma and ImaGene   Laura Miozzi
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Steffen Moeller
• [BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"   Amin Moghaddasi
• [BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"   Amin Moghaddasi
• [BioC] automating makeContrasts call in limma   Amin Moghaddasi
• [BioC] adapt exprSet class   Martin Morgan
• [BioC] limma for R 2.6   Martin Morgan
• [BioC] limma for R 2.6   Martin Morgan
• [BioC] limma for R 2.6   Martin Morgan
• [BioC] topTable threshold on p-value and logFC [Re: was design matrix]   Martin Morgan
• [BioC] One-Color Aglent Data into Limma GUI   Martin Morgan
• [BioC] newbie Q about object identity   Martin Morgan
• [BioC] biocLite() and getBioC scripts install development packages!   Martin Morgan
• [BioC] GO classification   Martin Morgan
• [BioC] BeadExplorer error   Martin Morgan
• [BioC] suppress messages in rma   Martin Morgan
• [BioC] creating expression set   Martin Morgan
• [BioC] Subsetting data from RGList (Again)   Martin Morgan
• [BioC] Subsetting data from RGList (Again)   Martin Morgan
• [BioC] Subsetting data from RGList (Again)   Martin Morgan
• [BioC] creating expression set   Martin Morgan
• [BioC] lmFit Error: "comparison of these types is not implemented"   Martin Morgan
• [BioC] R crashes after image array plots hgu133plus2 in R2.6.0   Martin Morgan
• [BioC] Gene Set Analysis on spotted data?   Tarun Nayar
• [BioC] Human whole genome Codelink arrays and paired analysis   Matthew Neville
• [BioC] Statistical Microarray and R courses at Imperial College   North, Bernard V
• [BioC] Time-point analysis   Mª José Nueda
• [BioC] MaSigPro   Mª José Nueda
• [BioC] Normalization with a reference sample   Olivier Nuñez
• [BioC] Breakpoints   Olivier Nuñez
• [BioC] modify CDF file for array study   Michal Okoniewski
• [BioC] makePDpackage: Problem loading PD package in oligo: read.celfiles function   Gayla Olbricht
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Gayla Olbricht
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Gayla Olbricht
• [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function   Gayla Olbricht
• [BioC] suppress messages in rma   Georg Otto
• [BioC] microRNA microarray analysis   Philipp Pagel
• [BioC] AnnBuilder: problem with kegg url?   Herve Pages
• [BioC] Bioconductor 2.1 is released   Herve Pages
• [BioC] Location of Bioconductor R package "TaqGCN"   Herve Pages
• [BioC] [Bioc-devel] Bioconductor 2.1 is released   Herve Pages
• [BioC] sequence search using a position weight matrix?   Herve Pages
• [BioC] GOstats install error under Linux Debian   Herve Pages
• [BioC] GOstats install error under Linux Debian   Herve Pages
• [BioC] BSgenome.Mmusculus.UCSC.mm8 and BSgenome   Herve Pages
• [BioC] Is a number within a set of ranges?   Herve Pages
• [BioC] Rgraphviz edge attributes can't be changed on Mac   Herve Pages
• [BioC] OntoCompare Error   Paquet, Agnes
• [BioC] Package installation error   Fabio Passetti
• [BioC] Download problem   Fabio Passetti
• [BioC] Download problem   Fabio Passetti
• [BioC] AMDA Update   Mattia Pelizzola
• [BioC] suppress messages in rma   Roger Peng
• [BioC] warning message in KS test   Francois Pepin
• [BioC] warning message in KS test   Francois Pepin
• [BioC] bioconductor installation problem   Olivier RICHE
• [BioC] bioconductor installation problem   Olivier RICHE
• [BioC] warning message in KS test   Adaikalavan Ramasamy
• [BioC] QC Parameter File error   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] AMDA Update   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] beadarray - bead level image plots   Matt Ritchie
• [BioC] bead level data, readIllumina   Matt Ritchie
• [BioC] bead level data, readIllumina   Matt Ritchie
• [BioC] Bead Array   Matt Ritchie
• [BioC] About the three weights in limma   Matt Ritchie
• [BioC] Problem reading data with beadarray package   Matt Ritchie
• [BioC] beadarray error: Did not find a slot called : se.exprs   Matt Ritchie
• [BioC] Error: could not find function "normaliseIllumina"[beadarray package]   Matt Ritchie
• [BioC] reading many affy U133 Plus_2.0   Mark Robinson
• [BioC] package for human ST gene arrays?   Mark Robinson
• [BioC] lmFit Error: "comparison of these types is not implemented"   Jose Rodriguez
• [BioC] MaSigPro   Narinder Singh Sahni
• [BioC] GeneNet   Narinder Singh Sahni
• [BioC] Newbie question - re reading imagene intensity files   Sally
• [BioC] Arguments for normalizewithinarrays (Limma)   Sally
• [BioC] loess and limma   Sally
• [BioC] GOstats: Coloring nodes in the induced GO graph   Deepayan Sarkar
• [BioC] limmaGUI and Agilent output files!   Keith Satterley
• [BioC] reading many affy U133 Plus_2.0   Holger Schwender
• [BioC] GOStats/RBGL installation error   Nicolas Servant
• [BioC] GOStats/RBGL installation error   Nicolas Servant
• [BioC] GOStats/RBGL installation error   Nicolas Servant
• [BioC] GOStats/RBGL installation error   Nicolas Servant
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for   Matt Settles
• [BioC] makePDpackage: Problem loading PD package in, oligo:read.celfiles function   Matt Settles
• [BioC] DNAString ("GC") -- error in nchar? [resolved]   Paul Shannon
• [BioC] sequence search using a position weight matrix?   Paul Shannon
• [BioC] KEGG & hyperGTest: an example?   Paul Shannon
• [BioC] KEGG & hyperGTest: an example?   Paul Shannon
• [BioC] GSEAbase example? [was KEGG & hyperGTest: an example?]   Paul Shannon
• [BioC] duplicateCorrelation dye-swap technical replicates   Roberta Sirovich
• [BioC] How to create nested data frames   Oleg Sklyar
• [BioC] Is a number within a set of ranges?   Oleg Sklyar
• [BioC] Is a number within a set of ranges?   Oleg Sklyar
• [BioC] Is a number within a set of ranges?   Oleg Sklyar
• [BioC] annaffy - saveHTML changed behaviour in newer versions   Colin A. Smith
• [BioC] annaffy - saveHTML changed behaviour in newer versions   Colin A. Smith
• [BioC] GOstats: Coloring nodes in the induced GO graph   Tim Smith
• [BioC] semi-supervised clustering   Tim Smith
• [BioC] semi-supervised clustering   Tim Smith
• [BioC] topTable threshold on p-value and logFC [Re: was design matrix]   Gordon Smyth
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Gordon Smyth
• [BioC] limma now on Bioconductor only, not CRAN   Gordon Smyth
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)   Gordon Smyth
• [BioC] residuals.MArrayLM   Gordon Smyth
• [BioC] residuals.MArrayLM   Gordon Smyth
• [BioC] residuals.MArrayLM   Gordon Smyth
• [BioC] Time-point analysis   Gordon Smyth
• [BioC] Arguments for normalizewithinarrays (Limma)   Gordon Smyth
• [BioC] lumi: LumiBatch slots don't match documentation   Gordon Smyth
• [BioC] automating makeContrasts call in limma   Gordon Smyth
• [BioC] duplicateCorrelation dye-swap technical replicates   Gordon Smyth
• [BioC] lumi::lumiR parseColumnName behaves unexpectedly   Gordon Smyth
• [BioC] lumi: how is the controlData to be read and used?   Gordon Smyth
• [BioC] lumi: how is the controlData to be read and used?   Gordon Smyth
• [BioC] lumi: how is the controlData to be read and used?   Gordon Smyth
• [BioC] About ndups error chol(V)   Gordon Smyth
• [BioC] lumi: how is the controlData to be read and used?   Gordon Smyth
• [BioC] contrasts in limma and missing values   Gordon Smyth
• [BioC] lmFit Error: "comparison of these types is not implemented"   Gordon Smyth
• [BioC] re About ndups error chol(V)   Gordon Smyth
• [BioC] design matrix   Lev Soinov
• [BioC] design matrix   Lev Soinov
• [BioC] All 3' UTRs for an organism - biomaRt package   Steffen
• [BioC] Biomart query in Web interface Vs. biomaRt package?   Steffen
• [BioC] Biomart query in Web interface Vs. biomaRt package?   Steffen
• [BioC] probelm of column names when using biomaRt   Steffen
• [BioC] markersymol filter problem   Steffen
• [BioC] affxparser fails to convert AGCC format cel file   Steiner, Guido
• [BioC] affxparser fails to convert AGCC format cel file   Steiner, Guido
• [BioC] affxparser fails to convert AGCC format cel file   Steiner, Guido
• [BioC] affxparser fails to convert AGCC format cel file   Steiner, Guido
• [BioC] affxparser fails to convert AGCC format cel file   Steiner, Guido
• [BioC] VSN, RMA, dCHIP, etc....   Tobias Straub
• [BioC] limma2biomaRt error   Mayte Suarez-Farinas
• [BioC] Air Turkey 2008 Angebote.   Sueden.
• [BioC] beadarray error: Did not find a slot called : se.exprs   Yogi Sundaravadanam
• [BioC] beadarray error: Did not find a slot called : se.exprs   Yogi Sundaravadanam
• [BioC] Error: could not find function "normaliseIllumina" [beadarray package]   Yogi Sundaravadanam
• [BioC] hugene10stv1probe?   Dan Swan
• [BioC] hugene10stv1probe?   Dan Swan
• [BioC] Agilent 4x44 single color expression arrays   Ido M. Tamir
• [BioC] Agilent 4x44 single color expression arrays   Ido M. Tamir
• [BioC] request for simple usage of probe level normalisations   Ido M. Tamir
• [BioC] HELP! lmFit and duplicateCorrelation   Ido M. Tamir
• [BioC] One-Color Aglent Data into Limma GUI   Ido M. Tamir
• [BioC] simpleaffy 2.14.02, setQCEnvironment   Stefan Thomsen
• [BioC] AffyExpress: AffyQA incompatible with simpleaffy 2.14.04?   Stefan Thomsen
• [BioC] VSN, RMA, dCHIP, etc....   Stefan Thomsen
• [BioC] VSN: narrowing down probe sets for parameter estimation   Stefan Thomsen
• [BioC] CEL files with different size   Joern Toedling
• [BioC] Summarization methods for affy genechip expression data   Joern Toedling
• [BioC] Is a number within a set of ranges?   Joern Toedling
• [BioC] clustering methods for gene expression   Donna Toleno
• [BioC] ctc package - cluster dendrogram   Donna Toleno
• [BioC] ctc package - cluster dendrogram   Donna Toleno
• [BioC] creating expression set   Yolande Tra
• [BioC] creating expression set   Yolande Tra
• [BioC] Annotation package for Yeast Genome S98 array ?   Alex Tsoi
• [BioC] YGS98 package does not provide locus link ID information ?   Alex Tsoi
• [BioC] ctc package - cluster dendrogram   Jarno Tuimala
• [BioC] Is a number within a set of ranges?   Artur Veloso
• [BioC] adapt exprSet class   Vosse, S.J.
• [BioC] processCGH in snapCGH package   Wang, Jianmin
• [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for   Gregory. R. Warnes
• [BioC] Rgraphviz edge attributes can't be changed on Mac   Luo Weijun
• [BioC] illumina annotation package error   Wayne Xu
• [BioC] illumina annotation package error   Wayne Xu
• [BioC] illumina annotation package error   Wayne Xu
• [BioC] AnnBuilder problem   Yihuan Xu
• [BioC] modify CDF file for array study   Hyuna Yang
• [BioC] Postdoc position in statistical genetics/genomics, UCSF Epidemiology & Biostatistics   Ru-Fang Yeh
• [BioC] print layout for Agilent data?   Yong Yin
• [BioC] print layout for Agilent data?   Yong Yin
• [BioC] Opinions on array design, normalization, and linear modeling with LIMMA   Yong Yin
• [BioC] Annotation package for Yeast Genome S98 array ?   John Zhang
• [BioC] u133aaofav2   Simens Zhong
• [BioC] u133aaofav2   Simens Zhong
• [BioC] How to create nested data frames   lgautier at altern.org
• [BioC] bead level data, readIllumina   marian.thieme at arcor.de
• [BioC] bead level data, readIllumina   marian.thieme at arcor.de
• [BioC] CEL files with different size   apolyzos at bioacademy.gr
• [BioC] affxparser fails to convert AGCC format cel file   bmb at bmbolstad.com
• [BioC] affxparser fails to convert AGCC format cel file   bmb at bmbolstad.com
• [BioC] affxparser fails to convert AGCC format cel file   bmb at bmbolstad.com
• [BioC] predict vsn with reference   chrisk
• [BioC] package for human ST gene arrays?   cstrato
• [BioC] Limma: Normalization with large numbers of differentially expressed genes   J.delasHeras at ed.ac.uk
• [BioC] One-Color Agilent Data into Limma GUI   J.delasHeras at ed.ac.uk
• [BioC] RE : Limma: Normalization with large numbers ofdifferentially expressed genes   J.delasHeras at ed.ac.uk
• [BioC] microRNA microarray analysis   J.delasHeras at ed.ac.uk
• [BioC] Arguments for normalizewithinarrays (Limma)   J.delasHeras at ed.ac.uk
• [BioC] Location of Bioconductor R package "TaqGCN"   young1 at email.unc.edu
• [BioC] Installing BioC + R 2.6: warnings   hpages at fhcrc.org
• [BioC] biocLite() and getBioC scripts install development packages!   hpages at fhcrc.org
• [BioC] bioconductor installation problem   hpages at fhcrc.org
• [BioC] BSgenome.Mmusculus.UCSC.mm8 and BSgenome   hpages at fhcrc.org
• [BioC] One-Color Aglent Data into Limma GUI   elliot harrison
• [BioC] One-Color Agilent Data into Limma GUI   elliot harrison
• [BioC] 2 Test Samples on 1 Array   elliot harrison
• [BioC] Extracting data sub set from loaded data.   elliott harrison
• [BioC] Extracting data sub set from loaded data.   elliott harrison
• [BioC] Subsetting data from RGList (Again)   elliott harrison
• [BioC] Subsetting data from RGList (Again)   elliott harrison
• [BioC] Subsetting data from RGList (Again)   elliott harrison
• [BioC] I played with this for hours   michel.pichon at hkusua.hku.hk
• [BioC] RNA degradation and no diff expressed genes   brini.elena at hsr.it
• [BioC] reading many affy U133 Plus_2.0   darteta001 at ikasle.ehu.es
• [BioC] GOStats/RBGL installation error   Li.Long at isb-sib.ch
• [BioC] GOStats/RBGL installation error   Li.Long at isb-sib.ch
• [BioC] running time of snapCGH processCGH and runDNAcopy   jhs1jjm at leeds.ac.uk
• [BioC] snapCGH: log2ratio   jhs1jjm at leeds.ac.uk
• [BioC] snapCGH: log2ratio   jhs1jjm at leeds.ac.uk
• [BioC] segmentation aCGH data   jhs1jjm at leeds.ac.uk
• [BioC] segmentation aCGH data   jhs1jjm at leeds.ac.uk
• [BioC] segmentation aCGH data   jhs1jjm at leeds.ac.uk
• [BioC] segmentation aCGH data   jhs1jjm at leeds.ac.uk
• [BioC] Biomart query in Web interface Vs. biomaRt package?   J.J.P.Lebrec at lumc.nl
• [BioC] Biomart query in Web interface Vs. biomaRt package?   J.J.P.Lebrec at lumc.nl
• [BioC] Chromosome 23 and 24 dropped after run snapCGH processCGH   caiwei at mdanderson.org
• [BioC] running time of snapCGH processCGH and runDNAcopy   caiwei at mdanderson.org
• [BioC] snapCGH: log2ratio   caiwei at mdanderson.org
• [BioC] snapCGH: log2ratio   caiwei at mdanderson.org
• [BioC] BMEI 2008, Sanya, China: Deadline 10 November   fu. qi.lai
• [BioC] About beadarray package   ssls sddd
• [BioC] About beadarray package   ssls sddd
• [BioC] About beadarray package   ssls sddd
• [BioC] semi-supervised clustering   friedrich.leisch at stat.uni-muenchen.de
• [BioC] semi-supervised clustering   friedrich.leisch at stat.uni-muenchen.de
• [BioC] Summarization methods for affy genechip expression data   zhi.zhang at syngenta.com
• [BioC] error message in gcrma   yzhang at vbi.vt.edu
• [BioC] error message in gcrma   yzhang at vbi.vt.edu
• [BioC] Plotting question: how to plot SNP location data?   Lauri.Nikkinen at veripalvelu.fi
• [BioC] Plotting question: how to plot SNP location data?   Lauri.Nikkinen at veripalvelu.fi
• [BioC] Question about getSnpAnnotation() in SNPchip Package   gao zhangg
• [BioC] maSigPro questions   Ingrid H. G. Østensen
• [BioC] Illumina replicates - packages   Ingrid H. G. Østensen
• [BioC] maSigPro questions   Ingrid H. G. Østensen
• [BioC] maSigPro: error?   Ingrid H. G. Østensen
• [BioC] About ndups error chol(V)   赵烨
• [BioC] re About ndups error chol(V)   赵烨

Last message date: Wed Oct 31 23:59:29 CET 2007
Archived on: Wed Oct 31 23:57:27 CET 2007

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