March 2011 Archives by date

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Starting: Tue Mar 1 00:06:12 CET 2011
Ending: Thu Mar 31 22:27:21 CEST 2011
Messages: 594

• [BioC] GO with R and Bioconductor   Duke
• [BioC] rpy save session and package downloads   rna seq
• [BioC] rpy save session and package downloads   Sean Davis
• [BioC] rpy save session and package downloads   Steve Lianoglou
• [BioC] edgeR glm fit error   Gordon K Smyth
• [BioC] rpy save session and package downloads   Hervé Pagès
• [BioC] rpy save session and package downloads   Pete Shepard
• [BioC] SNPlocs.Hsapiens.dbSNP.20101109 won't load   Pete Shepard
• [BioC] SNPlocs.Hsapiens.dbSNP.20101109 won't load   Sean Davis
• [BioC] Which resources for pathway analysis?   laurent jacob
• [BioC] edgeR glm fit error   Gordon K Smyth
• [BioC] error in bioconductor installation   Steve Lianoglou
• [BioC] Distribution of negative controls on Illumina HT12-v4 chips   Arnar Flatberg
• [BioC] error in bioconductor installation   kalesh karun
• [BioC] Which resources for pathway analysis?   January Weiner
• [BioC] Area-proportional Venn diagrams   January Weiner
• [BioC] Area-proportional Venn diagrams   Diego Diez
• [BioC] Mapping microarray probes to the genome using findOverlaps   Pages, Herve
• [BioC] Area-proportional Venn diagrams   Heidi Dvinge
• [BioC] GenomicFeatures: makeGeneDbFromBiomart()   Hooiveld, Guido
• [BioC] Mapping microarray probes to the genome using findOverlaps   Sean Davis
• [BioC] error in bioconductor installation   Steve Lianoglou
• [BioC] ChIPpeakAnno settings   Zhu, Lihua (Julie)
• [BioC] FlowViz xyplot event limit   Roger Leigh
• [BioC] FlowCore/FlowViz issues   Roger Leigh
• [BioC] iFlow and current Bioconductor release   Gabriel Nathan Kaufman, Mr
• [BioC] FlowViz xyplot event limit   Davide Rambaldi
• [BioC] FlowViz xyplot event limit   Finak, Greg
• [BioC] linking metabolites to pathway (KEGG)   viritha kaza
• [BioC] Distance to Feature   Zhu, Lihua (Julie)
• [BioC] Distance to Feature   Sarah Sheppard
• [BioC] Distance to Feature   Zhu, Lihua (Julie)
• [BioC] Distribution of negative controls on Illumina HT12-v4 chips   Wei Shi
• [BioC] insert Ns for repeat masked regions   rna seq
• [BioC] Plotting multiple graphs with a heatmap   Fong Chun Chan
• [BioC] Mapping microarray probes to the genome using findOverlaps   Hervé Pagès
• [BioC] Detection calls and LIMMA   Gordon K Smyth
• [BioC] Reading GFF using Starr   Feseha Abebe-Akele
• [BioC] PairwiseAlignedXStringSet from pre-aligned sequence   Jonathan Flowers
• [BioC] Plotting multiple graphs with a heatmap   Steve Lianoglou
• [BioC] insert Ns for repeat masked regions   Steve Lianoglou
• [BioC] RNASeq, differential expression between group, and large variance within groups   Gordon K Smyth
• [BioC] insert Ns for repeat masked regions   Pages, Herve
• [BioC] Extracting top upregulated genes from Limma analysis   Casper Shyr
• [BioC] HTqPCR: new qPCRset objects problem   Wenbo Mu
• [BioC] RNASeq, differential expression between group, and large variance within groups   Gordon K Smyth
• [BioC] Problems with IlluminaHumanMethylation27k.db   Francesco Mancuso
• [BioC] Extracting top upregulated genes from Limma analysis   Sean Davis
• [BioC] Plotting multiple graphs with a heatmap   Kevin R. Coombes
• [BioC] build Genome version   Elodie Chapeaublanc
• [BioC] edgeR: common.dispersion V/s tagwise.dispersion   Sridhara Gupta Kunjeti
• [BioC] heatmap.2 and makeContrasts   Supriya Munshaw
• [BioC] affymetrix miRNA QC Tool vs expresso data discrepancy   Giacomo Tuana
• [BioC] Affymetrix microarray normalization based on hybridization spikes   federico.comoglio
• [BioC] build Genome version   Fong Chun Chan
• [BioC] Detection calls and LIMMA   Richard Friedman
• [BioC] Question for NGS seq data (time couse)   Xing Li
• [BioC] Extracting top upregulated genes from Limma analysis   Noah Dowell
• [BioC] Overlapping boxplots with transparency   Fong Chun Chan
• [BioC] imageplot error message   Ina Hoeschele
• [BioC] Detection calls and LIMMA   Jenny Drnevich
• [BioC] RMA in Bioconductor versus APT - missing probesets   Mark Cowley
• [BioC] Overlapping boxplots with transparency   Heidi Dvinge
• [BioC] HTqPCR: new qPCRset objects problem   Heidi Dvinge
• [BioC] Overlapping boxplots with transparency   Fong Chun Chan
• [BioC] Drawing segments from one plot to another   Fong Chun Chan
• [BioC] HTqPCR: new qPCRset objects problem   Wenbo Mu
• [BioC] GenomicFeatures: makeGeneDbFromBiomart()   Marc Carlson
• [BioC] GGtools and GGBase installation problems   Neel Aluru
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Pages, Herve
• [BioC] PhD position in statistical bioinformatics   David Edwards
• [BioC] Extracting top upregulated genes from Limma analysis   Iain Gallagher
• [BioC] imageplot error message   Mike Smith
• [BioC] GGtools and GGBase installation problems   Vincent Carey
• [BioC] GenomicFeatures: makeGeneDbFromBiomart()   Hooiveld, Guido
• [BioC] Category R CMD check and not reloading required packages   Robert M. Flight
• [BioC] GGtools and GGBase installation problems   Neel Aluru
• [BioC] Category R CMD check and not reloading required packages   Sean Davis
• [BioC] Affymetrix microarray normalization based on hybridization spikes   James W. MacDonald
• [BioC] Category R CMD check and not reloading required packages   Martin Morgan
• [BioC] affymetrix miRNA QC Tool vs expresso data discrepancy   James W. MacDonald
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Chris Fields
• [BioC] Category R CMD check and not reloading required packages   Robert M. Flight
• [BioC] Drawing segments from one plot to another   Steve Lianoglou
• [BioC] Category R CMD check and not reloading required packages   Martin Morgan
• [BioC] RMA in Bioconductor versus APT - missing probesets   Michal Blazejczyk
• [BioC] RMA in Bioconductor versus APT - missing probesets   Vincent Carey
• [BioC] Error in solveUserSEW0 when using get.targets in TEQC   Johanna Hasmats
• [BioC] heatmap.2 and makeContrasts   James W. MacDonald
• [BioC] oligo package   YBao
• [BioC] oligo package   Dan Tenenbaum
• [BioC] heatmap.2 and makeContrasts   James W. MacDonald
• [BioC] RMA in Bioconductor versus APT - missing probesets   Mark Cowley
• [BioC] edgeR - tagwise dispersion   Sridhara Gupta Kunjeti
• [BioC] edgeR - tagwise dispersion   Davis McCarthy
• [BioC] edgeR - tagwise dispersion   Mark Robinson
• [BioC] edgeR - tagwise dispersion   Sridhara Gupta Kunjeti
• [BioC] edgeR - tagwise dispersion   Sridhara Gupta Kunjeti
• [BioC] edgeR - tagwise dispersion   Mark Robinson
• [BioC] edgeR - tagwise dispersion   Sridhara Gupta Kunjeti
• [BioC] quality control of affy Chips for miRNA   Assa Yeroslaviz
• [BioC] nested effects?   Naomi Altman
• [BioC] RNASeq, differential expression between group, and large variance within groups   Naomi Altman
• [BioC] FlowViz xyplot event limit   Roger Leigh
• [BioC] Can I know the number of genes in enriched GO category using GOseq   Biase, Fernando
• [BioC] heatmap.2 and makeContrasts   Wolfgang Huber
• [BioC] Reading GFF using Starr   Wolfgang Huber
• [BioC] stuck in biocLite("GEOquery")   Jack Luo
• [BioC] stuck in biocLite("GEOquery")   Dan Tenenbaum
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Hervé Pagès
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Cook, Malcolm
• [BioC] stuck in biocLite("GEOquery")   Jack Luo
• [BioC] stuck in biocLite("GEOquery")   Dan Tenenbaum
• [BioC] Reading GFF using Starr   Feseha Abebe-Akele
• [BioC] RNASeq, differential expression between group, and large variance within groups   Gordon K Smyth
• [BioC] PairwiseAlignedXStringSet from pre-aligned sequence   Hervé Pagès
• [BioC] Reading GFF using Starr   Wolfgang Huber
• [BioC] build Genome version   Marc Carlson
• [BioC] GenomicFeatures: makeGeneDbFromBiomart()   Marc Carlson
• [BioC] PairwiseAlignedXStringSet from pre-aligned sequence   Jonathan Flowers
• [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn   Hari Easwaran
• [BioC] edgeR   Sridhara Gupta Kunjeti
• [BioC] edgeR   Sridhara Gupta Kunjeti
• [BioC] edgeR   Mark Robinson
• [BioC] failed installation of bioClite   Louis Peperzak
• [BioC] GO.db for DO   Matthew Pocock
• [BioC] failed installation of bioClite   Martin Morgan
• [BioC] GO.db for DO   Matthew Pocock
• [BioC] GO.db for DO   Martin Morgan
• [BioC] GO.db for DO   Matthew Pocock
• [BioC] crlmm error in Mac OS   Steven Buechler
• [BioC] crlmm error in Mac OS   Vincent Carey
• [BioC] edgeR   Sridhara Gupta Kunjeti
• [BioC] lookUp for other terminologies   Matthew Pocock
• [BioC] lookUp for other terminologies   Martin Morgan
• [BioC] imageplot error message   Ina Hoeschele
• [BioC] Affy normalization and filtering method   Juliet Hannah
• [BioC] Problem with texi2dvi   Casper Shyr
• [BioC] heatmap.2 how to remove row separator   Deepayan Sarkar
• [BioC] lookUp for other terminologies   Matthew Pocock
• [BioC] lookUp for other terminologies   Vincent Carey
• [BioC] Please advice   Naomi Altman
• [BioC] Problem with texi2dvi   James W. MacDonald
• [BioC] Problem with texi2dvi   Kasper Daniel Hansen
• [BioC] QC for st gene arrays   YBao
• [BioC] [Bioc-sig-seq] SRAdb and getFastq   Jack Zhu
• [BioC] QC for st gene arrays   Benilton Carvalho
• [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn   Hari Easwaran
• [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn   axel.klenk at actelion.com
• [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn   Martin Morgan
• [BioC] Detection calls and LIMMA in GENE ST1.0   Richard Friedman
• [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn   Hari Easwaran
• [BioC] Detection calls and LIMMA in GENE ST1.0   James W. MacDonald
• [BioC] Detection calls and LIMMA in GENE ST1.0   Samuel Wuest
• [BioC] Detection calls and LIMMA in GENE ST1.0   cstrato
• [BioC] Perl/BioPerl   Simon Noël
• [BioC] Detection calls and LIMMA in GENE ST1.0   Richard Friedman
• [BioC] RE : Perl/BioPerl   Simon Noël
• [BioC] Problem with texi2dvi   Ying Wu
• [BioC] RE : Perl/BioPerl   Dan Tenenbaum
• [BioC] stuck in biocLite("GEOquery")   Dan Tenenbaum
• [BioC] GenomicFeatures install error on developement version   Paul Leo
• [BioC] GenomicFeatures install error on developement version   Martin Morgan
• [BioC] GenomicFeatures install error on developement version   Paul Leo
• [BioC] Problem with texi2dvi   Casper Shyr
• [BioC] Mapping microarray probes to the genome using findOverlaps   Ravi Karra
• [BioC] Can I know the number of genes in enriched GO category using GOseq   Matthew Young
• [BioC] Lumi problem   mali salmon
• [BioC] Lumi problem   mali salmon
• [BioC] Mapping microarray probes to the genome using findOverlaps   Benilton Carvalho
• [BioC] Anotation is not an equivalence (question regarding mouse4302.db and simmilar packages)   Vojtech Kulvait
• [BioC] Anotation is not an equivalence (question regarding mouse4302.db and simmilar packages) - correction   Vojtech Kulvait
• [BioC] Biocore Data Team : package mouse4302.db bug   Vojtech Kulvait
• [BioC] Mapping microarray probes to the genome using findOverlaps   Ravi Karra
• [BioC] HTqPCR: new qPCRset objects problem   Heidi Dvinge
• [BioC] GLMs in DESeq   Seanna McTaggart
• [BioC] From exon array CEL to XMAP annotation, what am I missing?   ekspiulo
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Biase, Fernando
• [BioC] Fwd: Lumi problem of adding control data   Pan Du
• [BioC] Lumi problem of adding control data   Pan Du
• [BioC] From exon array CEL to XMAP annotation, what am I missing?   Fong Chun Chan
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Fong Chun Chan
• [BioC] Lumi problem of adding control data   mali salmon
• [BioC] IPI to entrez id   Dick Beyer
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Vincent Carey
• [BioC] Lumi problem   Davis, Wade
• [BioC] crlmm error in Mac OS   Hervé Pagès
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Hervé Pagès
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Hervé Pagès
• [BioC] GenomicFeatures install error on developement version   Hervé Pagès
• [BioC] Mapping microarray probes to the genome using findOverlaps   Hervé Pagès
• [BioC] Error in solveUserSEW0 when using get.targets in TEQC   Hervé Pagès
• [BioC] Lumi problem   mali salmon
• [BioC] Help about 'pairwiseAlignment' in Biostrings package   ligang
• [BioC] Help on ChIPpeakAnno   Prashantha Hebbar
• [BioC] Help on ChIPpeakAnno   Prashantha Hebbar
• [BioC] Problems with IlluminaHumanMethylation27k.db - SOLVED   Francesco Mancuso
• [BioC] GLMs in DESeq   Simon Anders
• [BioC] Help on ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] differntially expressed gene   Prasad Siddavatam
• [BioC] Question for NGS seq data (time couse)   Naomi Altman
• [BioC] Problem with texi2dvi   Naomi Altman
• [BioC] Help on ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] graph classes: how to combine multiple graphs into a single graph   Paul Shannon
• [BioC] Biocore Data Team : package mouse4302.db bug   Marc Carlson
• [BioC] Help about 'pairwiseAlignment' in Biostrings package   Hervé Pagès
• [BioC] Anotation is not an equivalence (question regarding mouse4302.db and simmilar packages) - correction   Marc Carlson
• [BioC] find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list   Marc Carlson
• [BioC] DEGraph demo exprData question   Dick Beyer
• [BioC] IPI to entrez id   viritha kaza
• [BioC] differntially expressed gene   James W. MacDonald
• [BioC] linear mixed models using 'limma'   Tim Triche, Jr.
• [BioC] IPI to entrez id   Dick Beyer
• [BioC] Question for NGS seq data (time couse)   Davis McCarthy
• [BioC] Please advice   Naomi Altman
• [BioC] linear mixed models using 'limma'   Vincent Carey
• [BioC] IPI to entrez id   Marc Carlson
• [BioC] HTqPCR: new qPCRset objects problem   Wenbo Mu
• [BioC] IPI to entrez id   Marc Carlson
• [BioC] linear mixed models using 'limma'   Tim Triche, Jr.
• [BioC] Please advice   mali salmon
• [BioC] comparing HG-U219 data to HG-U133 data from public databases   Andreas Heider
• [BioC] comparing HG-U219 data to HG-U133 data from public databases   Sole Acha, Xavi
• [BioC] imageplot error message   Mike Smith
• [BioC] Dynamic Function creation   Davide Rambaldi
• [BioC] Dynamic Function creation   Davide Rambaldi
• [BioC] comparing HG-U219 data to HG-U133 data from public databases   Andreas Heider
• [BioC] Dynamic Function creation   Steve Lianoglou
• [BioC] [ENQUIRY] chIPpeakAnno annotatePeakInBatch   Zhu, Lihua (Julie)
• [BioC] [ENQUIRY] chIPpeakAnno annotatePeakInBatch   Zhu, Lihua (Julie)
• [BioC] Please advice   mali salmon
• [BioC] IPI to entrez id   Dick Beyer
• [BioC] HTqPCR: new qPCRset objects problem   Heidi Dvinge
• [BioC] Use of createSimpleBimap   Mark Dunning
• [BioC] IPI to entrez id   Marc Carlson
• [BioC] IPI to entrez id   Dick Beyer
• [BioC] Dynamic Function creation   Hervé Pagès
• [BioC] Use of createSimpleBimap   Tim Triche, Jr.
• [BioC] IPI to entrez id   viritha kaza
• [BioC] GLMs in DESeq (convergence problems)   Gordon K Smyth
• [BioC] DEGraph demo exprData question   Pierre Neuvial
• [BioC] Dynamic Function creation   Davide Rambaldi
• [BioC] GLMs in DESeq (convergence problems)   Seanna McTaggart
• [BioC] fastq files   David martin
• [BioC] fastq files   Martin Morgan
• [BioC] fastq files   David martin
• [BioC] fastq files   Martin Morgan
• [BioC] fastq files   David martin
• [BioC] DEGraph demo exprData question   Dick Beyer
• [BioC] DEGraph demo exprData question   Martin Morgan
• [BioC] How to detect and eliminate duplicate rows in an expression matrix in an automated way?   nqueralt at clinic.ub.es
• [BioC] Comparing datasets   viritha kaza
• [BioC] How to detect and eliminate duplicate rows in an expression matrix in an automated way?   Matthew McCall
• [BioC] How to model.matrix and makeContrasts for several groups with multiple treatments in limma?   Ou, Jianhong
• [BioC] fastq files   Hervé Pagès
• [BioC] DEGraph demo exprData question   laurent jacob
• [BioC] edgeR: calcNormFactors   Naomi Altman
• [BioC] edgeR: calcNormFactors   João Moura
• [BioC] edgeR: calcNormFactors   Neel Aluru
• [BioC] edgeR: calcNormFactors   Naomi Altman
• [BioC] How to model.matrix and makeContrasts for several groups with multiple treatments in limma?   Naomi Altman
• [BioC] Adding to GeneSetCollection object from function   Iain Gallagher
• [BioC] BioC 2.8 New Package Submission Deadline - 3/23/2011   Wong, Chao-Jen
• [BioC] Adding to GeneSetCollection object from function   Iain Gallagher
• [BioC] Reading GFF using Starr   zacher at lmb.uni-muenchen.de
• [BioC] Adding to GeneSetCollection object from function   Martin Morgan
• [BioC] Adding to GeneSetCollection object from function   Iain Gallagher
• [BioC] IRanges - Find   Fahim Mohammad
• [BioC] IRanges - Find   Martin Morgan
• [BioC] iFlow/flowCore installation problem   Gabriel Nathan Kaufman, Mr
• [BioC] iFlow/flowCore installation problem   Dan Tenenbaum
• [BioC] iFlow/flowCore installation problem   Gabriel Nathan Kaufman, Mr
• [BioC] iFlow/flowCore installation problem   Dan Tenenbaum
• [BioC] pairwiseAlignment generates different outcomes for the same input sequences   Alogmail2 at aol.com
• [BioC] Mapping microarray probes to the genome using findOverlaps   Ravi Karra
• [BioC] Separate channel analysis on connected design   Luis A. Alcaraz
• [BioC] gcrma - u133aaofav2probe error   Myrto Kostadima
• [BioC] Open Postdoc Positions   Thomas Girke
• [BioC] NMF, reproducing custom algorithm   Pavel Goldstein
• [BioC] pairwiseAlignment generates different outcomes for the same input sequences   Martin Morgan
• [BioC] Comparing datasets   Balasubramanian Ganesan
• [BioC] Comparing datasets   Pavel Goldstein
• [BioC] gcrma - u133aaofav2probe error   James W. MacDonald
• [BioC] xmapcore   ekspiulo
• [BioC] gcrma - u133aaofav2probe error   Henrik Bengtsson
• [BioC] pairwiseAlignment generates different outcomes for the same inp...   Alogmail2 at aol.com
• [BioC] iFlow/flowCore installation problem   Dan Tenenbaum
• [BioC] How do I parse HTML table using RCurl?   Ruppert Valentino
• [BioC] BioC 2.8 New Package Submission Deadline - 3/23/2011   Wong, Chao-Jen
• [BioC] Separate channel analysis on connected design   Naomi Altman
• [BioC] How do I parse HTML table using RCurl?   Sean Davis
• [BioC] pairwiseAlignment generates different outcomes for the same input sequences   Hervé Pagès
• [BioC] How do I parse HTML table using RCurl?   Dan Tenenbaum
• [BioC] How do I parse HTML table using RCurl?   James F. Reid
• [BioC] How do I parse HTML table using RCurl?   Ruppert Valentino
• [BioC] pairwiseAlignment generates different outcomes for the same input sequences   Pages, Herve
• [BioC] pairwiseAlignment generates different outcomes for the same input sequences   alogmail2 at aol.com
• [BioC] How do I parse HTML table using RCurl?   James F. Reid
• [BioC] An error while installing RWebService   MLSC MANIPAL
• [BioC] Open PhD position   Peter Robinson
• [BioC] xmapcore   Tim Yates
• [BioC] xmapcore   ekspiulo
• [BioC] openVignette(Biobase) and citation(Biobase) give errors after installing Biobase   Louis Peperzak
• [BioC] package for collapsing probe id to entrezid or gene symbols   Wendy Qiao
• [BioC] openVignette(Biobase) and citation(Biobase) give errors after installing Biobase   Vincent Carey
• [BioC] openVignette(Biobase) and citation(Biobase) give errors after installing Biobase   Dan Tenenbaum
• [BioC] An error while installing RWebService   Dan Tenenbaum
• [BioC] package for collapsing probe id to entrezid or gene symbols   James W. MacDonald
• [BioC] ancova function in package HH   Qian Liu
• [BioC] package for collapsing probe id to entrezid or gene symbols   Wendy Qiao
• [BioC] package for collapsing probe id to entrezid or gene symbols   Paul Geeleher
• [BioC] package for collapsing probe id to entrezid or gene symbols   Yong Li
• [BioC] Separate channel analysis on connected design   Luis A. Alcaraz
• [BioC] pairwiseAlignment generates different outcomes for the same inp...   Hervé Pagès
• [BioC] How do I parse HTML table using RCurl?   Geoff Jentry
• [BioC] limma design experiment   Luis Z
• [BioC] Calculate coverage on genome.   Fabrice Tourre
• [BioC] Calculate coverage on genome.   Fabrice Tourre
• [BioC] Calculate coverage on genome.   Martin Morgan
• [BioC] transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma   Gustavo Kijak
• [BioC] iFlow/flowCore installation problem   Dan Tenenbaum
• [BioC] limma2annaffy error   mali salmon
• [BioC] Calculate coverage on genome.   Fabrice Tourre
• [BioC] transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma   Mark Dunning
• [BioC] vector size issue in CGHMCR   nac
• [BioC] vector size issue in CGHMCR   Sean Davis
• [BioC] Discrepancies finding genes with a given GO term   Oscar Rueda
• [BioC] error while installing Java related packages   MLSC MANIPAL
• [BioC] iFlow/flowCore installation problem   Michael Lawrence
• [BioC] Calculate coverage on genome.   Martin Morgan
• [BioC] limma2annaffy error   James W. MacDonald
• [BioC] Calculate coverage on genome.   Fabrice Tourre
• [BioC] error while installing Java related packages   Martin Morgan
• [BioC] error while installing Java related packages   Martin Morgan
• [BioC] ancova function in package HH   Qian Liu
• [BioC] How to set variable to NOT NULL using RODBC package   Qian Liu
• [BioC] xmapcore   Tim Yates
• [BioC] ancova function in package HH   Hervé Pagès
• [BioC] flowStats quadrantGate and Back-Gating   Aric Gregson
• [BioC] transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma   Wei Shi
• [BioC] limma design experiment   Gordon K Smyth
• [BioC] How do I parse HTML table using RCurl?   Vivek Jayaswal
• [BioC] limma design experiment   Luis Z
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Michael Lawrence
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Pages, Herve
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Michael Lawrence
• [BioC] Mapping genomic coordinates to transcript coordinates? (revived)   Pages, Herve
• [BioC] Bug in gpls package?   Carlos J. Gil Bellosta
• [BioC] [Rd] tools::checkRd() output different from R CMD check   Dan Tenenbaum
• [BioC] Bug in package plsRglm?   Carlos J. Gil Bellosta
• [BioC] Are there any module could be used to convert a data.frame table to a matrix format.   a a
• [BioC] xmapcore   Tim Yates
• [BioC] Are there tools of LD/recombination rate measurement in R/bioconductor   Mao Jianfeng
• [BioC] limma2annaffy error   mali salmon
• [BioC] r/maanova error in matest()   Mike Walter
• [BioC] r/maanova error in matest()--post scriptum   Michael Walter
• [BioC] Go annotations   Assa Yeroslaviz
• [BioC] GO categories: how to extract a specific rank of the category-tree   AYeroslaviz
• [BioC] limma2annaffy error   James W. MacDonald
• [BioC] Go annotations   Marc Carlson
• [BioC] Get Gene annotation (GO terms)   David martin
• [BioC] Get Gene annotation (GO terms)   Marc Carlson
• [BioC] Get Gene annotation (GO terms)   David martin
• [BioC] Get Gene annotation (GO terms)   Marc Carlson
• [BioC] Get Gene annotation (GO terms)   Marc Carlson
• [BioC] choosing normalization method for RNA-seq analysis   Biase, Fernando
• [BioC] limma design experiment   Gordon K Smyth
• [BioC] importing ID table in AnnotationDbi   Dana.Stanley at csiro.au
• [BioC] Question about translate funciton in Biostrings package   ligang
• [BioC] Question about translate funciton in Biostrings package   Pages, Herve
• [BioC] Get Gene annotation (GO terms)   David martin
• [BioC] error while installing SJava   MLSC MANIPAL
• [BioC] Problem with hgu133plus2 probe installation   sneha patil
• [BioC] RE : Question about translate funciton in Biostrings package   Simon Noël
• [BioC] Agi4x44PreProcess /filtering probenames from GeneName   Maria Raeder
• [BioC] Problem with hgu133plus2 probe installation   James W. MacDonald
• [BioC] error while installing SJava   Martin Morgan
• [BioC] working with ROOT and the xps problem   Assa Yeroslaviz
• [BioC] GO categories: how to extract a specific rank of the category-tree   Assa Yeroslaviz
• [BioC] working with ROOT and the xps problem   cstrato
• [BioC] GO categories: how to extract a specific rank of the category-tree   Marc Carlson
• [BioC] importing ID table in AnnotationDbi   Marc Carlson
• [BioC] Query regarding matchprobes package   sneha patil
• [BioC] Query regarding matchprobes package   Wolfgang Huber
• [BioC] Agi4x44PreProcess /filtering probenames from GeneName   Wolfgang Huber
• [BioC] choosing normalization method for RNA-seq analysis   Wolfgang Huber
• [BioC] Query regarding matchprobes package   Kasper Daniel Hansen
• [BioC] Query regarding matchprobes package   Wolfgang Huber
• [BioC] readCtData() in HTqPCR with matrix of multiple samples   Andrew Yee
• [BioC] choosing normalization method for RNA-seq analysis   Biase, Fernando
• [BioC] How to generate Spot Types File?   Casper Shyr
• [BioC] readCtData() in HTqPCR with matrix of multiple samples   Heidi Dvinge
• [BioC] How to generate Spot Types File?   Maciej Jończyk
• [BioC] How to generate Spot Types File?   Casper Shyr
• [BioC] GenomeGraphs - plotting outside of axis   Lavinia Gordon
• [BioC] importing ID table in AnnotationDbi   Dana.Stanley at csiro.au
• [BioC] [Rocky] - GEOquery   하오잠 로
• [BioC] How to generate Spot Types File?   Maciej Jończyk
• [BioC] limma design problem with a two color dataset   Yong Li
• [BioC] preprocessCore "Undefined log2" installation error   Bruce Hayward
• [BioC] Human Gene 1.1 ST cdf   Nicolas Servant
• [BioC] plot.DNAcopy error   Nathalie Conte
• [BioC] Human Gene 1.1 ST cdf   James W. MacDonald
• [BioC] Human Gene 1.1 ST cdf   Nicolas Servant
• [BioC] preprocessCore "Undefined log2" installation error   bmb at bmbolstad.com
• [BioC] package for collapsing probe id to entrezid or gene symbols   Hervé Pagès
• [BioC] Mapping microarray probes to the genome using findOverlaps   Hervé Pagès
• [BioC] Mapping microarray probes to the genome using findOverlaps   Benilton Carvalho
• [BioC] Human Gene 1.1 ST cdf   James W. MacDonald
• [BioC] Human Gene 1.1 ST cdf   cstrato
• [BioC] Modeling of methylation status using lumi   Ina Hoeschele
• [BioC] EdgeR - Roast/Romer-like for digital gene expression   Jeff Hsu
• [BioC] Modeling of methylation status using lumi   Pan Du
• [BioC] readCtData() in HTqPCR with matrix of multiple samples   Andrew Yee
• [BioC] RE : Question about translate funciton in Biostrings package   ligang
• [BioC] Human Gene 1.1 ST cdf   Michal Blazejczyk
• [BioC] limma complex contrast matrix   Prasad Siddavatam
• [BioC] limma neqc   Ina Hoeschele
• [BioC] goseq KEGG testing?   Jenny Drnevich
• [BioC] lumi batch from genomestudio   kripa raman
• [BioC] create lumi batch from genomestudio data   Kripa R
• [BioC] limma neqc   Wei Shi
• [BioC] minor allele frequency of snps in hapmap database   Pete Shepard
• [BioC] minor allele frequency of snps in hapmap database   Benilton Carvalho
• [BioC] goseq KEGG testing?   Matthew Young
• [BioC] package for collapsing probe id to entrezid or gene symbols   Wendy Qiao
• [BioC] dealing with negative values in illumina   Prasad Siddavatam
• [BioC] create lumi batch from genomestudio data   amit mandal
• [BioC] DESeq variance stabilisation and clustering   Timothy Hughes
• [BioC] DESeq variance stabilisation and clustering   Timothy Hughes
• [BioC] DESeq variance stabilisation and clustering   Simon Anders
• [BioC] preprocessCore "Undefined log2" installation error   Bruce Hayward
• [BioC] limma neqc   Ina Hoeschele
• [BioC] Structural variations analysis   Vincenzo Capece
• [BioC] Structural variations analysis   Steve Lianoglou
• [BioC] mouse Entrez ids into human orthologous Entrez ids with inparanoid   Glazko, Galina V
• [BioC] limma neqc   Wei Shi
• [BioC] dealing with negative values in illumina   Wei Shi
• [BioC] limma design problem with a two color dataset   Gordon K Smyth
• [BioC] protein orthologs   Stefanie Carola Gerstberger
• [BioC] magetab2bioc error   pratibha mani
• [BioC] dealing with negative values in illumina   Simon Anders
• [BioC] Structural variations analysis   Vincenzo Capece
• [BioC] EdgeR GLM gene expression analysis of 3 groups   Shona Wood
• [BioC] lumi batch from genomestudio   Pan Du
• [BioC] dealing with negative values in illumina   Pan Du
• [BioC] magetab2bioc error   Wolfgang Huber
• [BioC] foreach, doMC, and GOstats problems   Tarca, Adi
• [BioC] foreach, doMC, and GOstats problems   Dan Tenenbaum
• [BioC] foreach, doMC, and GOstats problems   Benilton Carvalho
• [BioC] foreach, doMC, and GOstats problems   Tarca, Adi
• [BioC] foreach, doMC, and GOstats problems   Dan Tenenbaum
• [BioC] foreach, doMC, and GOstats problems   Dan Tenenbaum
• [BioC] foreach, doMC, and GOstats problems   Tarca, Adi
• [BioC] mouse Entrez ids into human orthologous Entrez ids with inparanoid   Marc Carlson
• [BioC] foreach, doMC, and GOstats problems   Dan Tenenbaum
• [BioC] Need Help With Factorial Design Matrix in Limma   Jonathan Harper
• [BioC] dealing with negative values in illumina   Wei Shi
• [BioC] EdgeR GLM gene expression analysis of 3 groups   Davis McCarthy
• [BioC] EdgeR GLM gene expression analysis of 3 groups   Mark Robinson
• [BioC] error while installing SJava   MLSC MANIPAL
• [BioC] Which is best among RWebServices and Rserve?   MLSC MANIPAL
• [BioC] Which is best among RWebServices and Rserve?   Amos Folarin
• [BioC] foreach, doMC, and GOstats problems   Tarca, Adi
• [BioC] Which is best among RWebServices and Rserve?   Martin Morgan
• [BioC] protein orthologs   Marc Carlson
• [BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST   M. Emily Merrill
• [BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST   cstrato
• [BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST   M. Emily Merrill
• [BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST   cstrato
• [BioC] Bioconductor with Affymetrix Mouse Gene 1.0 ST   Benilton Carvalho
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Richard Gill
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Martin Morgan
• [BioC] Calculate average of replicates   Wendy Qiao
• [BioC] average replicate columns in a matrix   Wendy Qiao
• [BioC] Access the probe ids associated with each cluster   Wendy Qiao
• [BioC] Access the probe ids associated with each cluster   Steve Lianoglou
• [BioC] Access the probe ids associated with each cluster   Wendy Qiao
• [BioC] average replicate columns in a matrix   Wolfgang Huber
• [BioC] Using Sample IDs from Sample Name column   Ross Haggart
• [BioC] Visualising the GO structure (RNA-seq) using topGO and goseq   Paolo Sonego
• [BioC] timecourse package - input data   silvia.heyde at med.uni-goettingen.de
• [BioC] Problem with oneChannelGUI   Guido Leoni
• [BioC] Problem with oneChannelGUI   Martin Morgan
• [BioC] Problem with oneChannelGUI   Guido Leoni
• [BioC] Problem with oneChannelGUI   Martin Morgan
• [BioC] goseq problem   Naomi Altman
• [BioC] Problem with oneChannelGUI   Steve Lianoglou
• [BioC] goseq problem   Naomi Altman
• [BioC] Problem with oneChannelGUI   Guido Leoni
• [BioC] Testing biased microarray data   January Weiner
• [BioC] Testing biased microarray data   Simon Anders
• [BioC] Using Sample IDs from Sample Name column   Heidi Dvinge
• [BioC] dealing with negative values in illumina   Mete Civelek
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Richard Gill
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Martin Morgan
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Kasper Daniel Hansen
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Kasper Daniel Hansen
• [BioC] Calculate average of replicates   James W. MacDonald
• [BioC] read gz compressed wig files?   Hamid Bolouri
• [BioC] problems installing lumi   Ina Hoeschele
• [BioC] Lapply for two GRanges objects?   Hollis Wright
• [BioC] problems installing lumi   Dan Tenenbaum
• [BioC] dealing with negative values in illumina   Wei Shi
• [BioC] average replicate columns in a matrix   Gordon K Smyth
• [BioC] Lapply for two GRanges objects?   Martin Morgan
• [BioC] goseq: gene universe   Naomi Altman
• [BioC] Rgraphviz windows version incompatible with current Graphviz   Richard Gill
• [BioC] Rsamtools problem   Vincenzo Capece
• [BioC] Problem with oneChannelGUI   rcaloger
• [BioC] Lapply for two GRanges objects?   Michael Lawrence
• [BioC] GoStats   David martin
• [BioC] Rsamtools problem   Martin Morgan
• [BioC] Rsamtools problem   Steve Lianoglou
• [BioC] average replicate columns in a matrix   Zhu, Lihua (Julie)
• [BioC] goseq: gene universe   Jenny Drnevich
• [BioC] Limma factorial experiment: interaction parameter   Donald Dunbar
• [BioC] Limma factorial experiment: interaction parameter   Oscar Rueda
• [BioC] Troubles installing pcaMethods on R2.12.1   Alfons Gonzalez
• [BioC] Custom CDF Version 14 is released   Manhong Dai
• [BioC] Lapply for two GRanges objects?   Hollis Wright
• [BioC] paired samples test in limma package   Yi, Ming (NIH/NCI) [C]
• [BioC] SNP retrieval between two mouse strains   sabrina
• [BioC] avereps function in limma (dealing with negative values in illumina)   Wei Shi
• [BioC] average replicate columns in a matrix   Gordon K Smyth
• [BioC] SNP retrieval between two mouse strains   Hervé Pagès
• [BioC] Visualising the GO structure (RNA-seq) using topGO and goseq   Marc Carlson
• [BioC] GoStats   Marc Carlson
• [BioC] LIMMA with beta distributed data   Steve Shen
• [BioC] XOR or intersect for several vectors   Wendy Qiao
• [BioC] XOR or intersect for several vectors   Carlos J. Gil Bellosta
• [BioC] Error in calling read.maimages   Casper Shyr
• [BioC] Problem with oneChannelGUI   Guido Leoni
• [BioC] GoStats   David martin
• [BioC] Limma factorial experiment: interaction parameter   Donald Dunbar
• [BioC] Visualising the GO structure (RNA-seq) using topGO, and goseq   Paolo Sonego
• [BioC] LIMMA with beta distributed data   Sunny Srivastava
• [BioC] average replicate columns in a matrix   Amos Folarin
• [BioC] GoStats and microRNA pipeline using Biomart   David martin
• [BioC] SNP retrieval between two mouse strains   Cook, Malcolm
• [BioC] SNP retrieval between two mouse strains   Benjamin King
• [BioC] memory problem to read CEL files   Xiaobin Yuan
• [BioC] GoStats and microRNA pipeline using Biomart   Steve Lianoglou
• [BioC] memory problem to read CEL files   Steve Lianoglou
• [BioC] SNP retrieval between two mouse strains   sabrina
• [BioC] GoStats and microRNA pipeline using Biomart   David martin
• [BioC] Chip-Seq tag density plot   Eva Benito Garagorri
• [BioC] Gene description   Mohamed Lajnef
• [BioC] memory problem to read CEL files   Martin Morgan
• [BioC] LIMMA with beta distributed data   Steve Shen
• [BioC] SNP retrieval between two mouse strains   Cook, Malcolm
• [BioC] Chip-Seq tag density plot   Vincent Carey
• [BioC] Error in calling read.maimages   Wolfgang Huber
• [BioC] memory problem to read CEL files   Xiaobin Yuan
• [BioC] GoStats and microRNA pipeline using Biomart   James F. Reid
• [BioC] Reading methylation data using lumi package   Yue Yu
• [BioC] LIMMA with beta distributed data   Sunny Srivastava
• [BioC] average replicate columns in a matrix   Yi, Ming (NIH/NCI) [C]
• [BioC] Gene description   James W. MacDonald
• [BioC] memory problem to read CEL files   Lenka Radova
• [BioC] GoStats and microRNA pipeline using Biomart   David martin
• [BioC] LIMMA with beta distributed data   Steve Shen
• [BioC] RE : memory problem to read CEL files   Simon Noël
• [BioC] RE : Gene description   Simon Noël
• [BioC] problems installing lumi   Ina Hoeschele
• [BioC] problems installing lumi   Dan Tenenbaum
• [BioC] problems installing lumi   Ina Hoeschele
• [BioC] problems installing lumi   Dan Tenenbaum
• [BioC] limma neqc   Ina Hoeschele
• [BioC] Chip-Seq tag density plot   Hervé Pagès
• [BioC] Reading methylation data using lumi package   Sean Davis
• [BioC] Reading methylation data using lumi package   Yue Yu
• [BioC] XOR or intersect for several vectors   Hervé Pagès
• [BioC] gff files: how to tell if right-open interval convention used?   karlerhard at berkeley.edu
• [BioC] gff files: how to tell if right-open interval convention used?   Hervé Pagès
• [BioC] gff files: how to tell if right-open interval convention used?   Chris Fields
• [BioC] limma neqc   Wei Shi
• [BioC] What is GO term   李天成
• [BioC] What is GO term   Philipp Pagel
• [BioC] Chip-Seq tag density plot   Eva Benito Garagorri
• [BioC] GoStats and microRNA pipeline using Biomart   James F. Reid
• [BioC] GoStats and microRNA pipeline using Biomart   David martin
• [BioC] edgeR - MDS plot   Sridhara Gupta Kunjeti
• [BioC] problem with biomaRt package using mart "snps", dataset "hsapiens_structvar", attribute "description"   mmaguire
• [BioC] GoStats and microRNA pipeline using Biomart   Iain Gallagher
• [BioC] Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling   Cook, Malcolm
• [BioC] Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling   Martin Morgan
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   adeonari at mrc-lmb.cam.ac.uk
• [BioC] read gz compressed wig files?   Steve Lianoglou
• [BioC] read gz compressed wig files?   Steve Lianoglou
• [BioC] GoStats and microRNA pipeline using Biomart   Marc Carlson
• [BioC] Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling   Cook, Malcolm
• [BioC] Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling   Cook, Malcolm
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   vasu punj

Last message date: Thu Mar 31 22:27:21 CEST 2011
Archived on: Thu Mar 31 22:27:36 CEST 2011

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