November 2011 Archives by date

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Starting: Tue Nov 1 01:13:07 CET 2011
Ending: Wed Nov 30 23:53:07 CET 2011
Messages: 551

• [BioC] Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?   Marc Carlson
• [BioC] annotation db for miRNA_2 Array   Marc Carlson
• [BioC] annotation db for miRNA_2 Array   Marc Carlson
• [BioC] problem with IGH genes in org.Hs.egCHRLOC   Francois Pepin
• [BioC] annotate histograms   Wendy Qiao
• [BioC] annotate histograms   Janet L Smith
• [BioC] annotate histograms   Kevin R. Coombes
• [BioC] How to use limma to do 2 factors with multiple level analysis   Zhi Zhang
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   shirley zhang
• [BioC] Bioconductor 2.9 is released   Dan Tenenbaum
• [BioC] problem with IGH genes in org.Hs.egCHRLOC   Marc Carlson
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   Hervé Pagès
• [BioC] how to use writeFASTA   wang peter
• [BioC] how to use writeFASTA   Martin Morgan
• [BioC] Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors   Wong, Chao-Jen
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   shirley zhang
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   shirley zhang
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   Sean Davis
• [BioC] goSeq error (steve Shen)   Alicia Oshlack
• [BioC] problem with IGH genes in org.Hs.egCHRLOC   Francois Pepin
• [BioC] visualise model fit in edgeR   Gordon K Smyth
• [BioC] Packages reproducing phylogenetic tree from output of MEGA   Dejian Zhao
• [BioC] objective criterion for identification of outlying arrays by pca   Richard Friedman
• [BioC] objective criterion for identification of outlying arrays by pca   James W. MacDonald
• [BioC] objective criterion for identification of outlying arrays by pca   Vincent Carey
• [BioC] Welcome to the "Bioconductor" mailing list   Adriana Munoz
• [BioC] MA plots for large number of arrays   Juliet Hannah
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] MA plots for large number of arrays   James W. MacDonald
• [BioC] meta analysis   Joao Fadista
• [BioC] MA plots for large number of arrays   James W. MacDonald
• [BioC] objective criterion for identification of outlying arrays by pca   Kevin R. Coombes
• [BioC] Error installing geneplotter   Ignacio Lopez de Ullibarri [guest]
• [BioC] Error installing geneplotter   Dan Tenenbaum
• [BioC] baySeq plotPosteriors or plotMA question   Smith, Hilary A
• [BioC] Welcome to the "Bioconductor" mailing list   Hervé Pagès
• [BioC] Welcome to the "Bioconductor" mailing list   Ramon Diaz-Uriarte
• [BioC] DESeq -SCVplot   Dawei Li
• [BioC] Normalization in Coverage   rohan bareja
• [BioC] lumi: Methylation450 Data Input   Jiayi Sun
• [BioC] baySeq plotPosteriors or plotMA question   Vincent Carey
• [BioC] Agi4x44Preprocess/Limma and number of significant p-values   Paulo Nuin
• [BioC] Agi4x44Preprocess/Limma and number of significant p-values   Wei Xu
• [BioC] bam or sam for counting   wang peter
• [BioC] bam or sam for counting   Martin Morgan
• [BioC] rtracklayer fails to load in the new Bioconductor devel branch   Ivan Gregoretti
• [BioC] rtracklayer fails to load in the new Bioconductor devel branch   Martin Morgan
• [BioC] bam or sam for counting   Sean Davis
• [BioC] an error to open bam file   wang peter
• [BioC] an error to open bam file   Martin Morgan
• [BioC] downloading GO from biomart through bioconductor   Brian Tsai
• [BioC] minfi F-test Results   Dario Strbenac
• [BioC] goSeq error   Matthew Young
• [BioC] goSeq error   Matthew Young
• [BioC] Use of glm for multivariate logistic regression of microarray data   Ruppert Valentino
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] Predicted overlaps of 3 gene lists   Edwin Groot
• [BioC] Re2:   danieladna
• [BioC] MA plots for large number of arrays   mjonczyk
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Oscar Flores
• [BioC] MA plots for large number of arrays   Martin Morgan
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Oscar Flores
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Martin Morgan
• [BioC] Bioinformatics/biostatistics position at the Institute of Cancer Research, UK   Daniel Brewer
• [BioC] Packages reproducing phylogenetic tree from output of MEGA   Ron Ophir
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] DESeq -SCVplot   Wolfgang Huber
• [BioC] Extracting variant nucleotides   Alpesh Querer
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   shirley zhang
• [BioC] lumi: Methylation450 Data Input   Wong, Chao-Jen
• [BioC] R/Bioc workshops on Dec 8-12 at UC Riverside   Thomas Girke
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   Sean Davis
• [BioC] Extracting variant nucleotides   Michael Lawrence
• [BioC] Extracting variant nucleotides   Valerie Obenchain
• [BioC] where to get chr_rpts file for dbSNP human 36.3 assembly   shirley zhang
• [BioC] Extracting variant nucleotides   Michael Lawrence
• [BioC] problem in normalizing single channel gar file   Niraj Nepal
• [BioC] edgeR for miRNA   Lana Schaffer
• [BioC] edgeR for miRNA   Mark Robinson
• [BioC] illuminaHumanv4 mappings   Valerie Deffontaine
• [BioC] edd deprecation   Tim Rayner
• [BioC] objective criterion for identification of outlying arrays by pca   Richard Friedman
• [BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS   Richard Friedman
• [BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS   Vincent Carey
• [BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS   Benilton Carvalho
• [BioC] Does liftOver work for SNPs mapping to different chr between different builds   shirley zhang
• [BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS   Richard Friedman
• [BioC] objective criterion for identification of outlying arrays by pca   Kevin R. Coombes
• [BioC] objective criterion for identification of outlying arrays by pca IN GENE ST1.0 CHIPS   cstrato
• [BioC] gene enrichment analysis without a control sample   Wendy Qiao
• [BioC] gene enrichment analysis without a control sample   Wu, Di
• [BioC] gene enrichment analysis without a control sample   Robert Castelo
• [BioC] gene enrichment analysis without a control sample   Wendy Qiao
• [BioC] downloading GO from biomart through bioconductor   Marc Carlson
• [BioC] gene enrichment analysis without a control sample   Wu, Di
• [BioC] Does liftOver work for SNPs mapping to different chr between different builds   Michael Lawrence
• [BioC] phenodata GEOquery query   Reema Singh
• [BioC] objective criterion for identification of outlying arrays by pca   shirley0818
• [BioC] phenodata GEOquery query   Sean Davis
• [BioC] edgeR and pair-wise comparison error by estimateGLMCommonDisp   Sheng [guest]
• [BioC] Convert gene expression matrix to ExpressionSet   Wendy Qiao
• [BioC] How to extract Phenotype data from GSE   Reema Singh
• [BioC] Convert gene expression matrix to ExpressionSet   Martin Morgan
• [BioC] Convert gene expression matrix to ExpressionSet   Wendy Qiao
• [BioC] Convert gene expression matrix to ExpressionSet   Martin Morgan
• [BioC] IlluminaHumanMethylation450k.db Reference Versions   Dario Strbenac
• [BioC] Convert gene expression matrix to ExpressionSet   Wendy Qiao
• [BioC] Convert gene expression matrix to ExpressionSet   Robert Castelo
• [BioC] edd deprecation   Vincent Carey
• [BioC] How to extract Phenotype data from GSE   James F. Reid
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] problem with using GSVA package   Wendy Qiao
• [BioC] problem with using GSVA package   Juan Roberto CASTELO VALDUEZA
• [BioC] problem with using GSVA package   Wendy Qiao
• [BioC] problem with using GSVA package   Robert Castelo
• [BioC] IlluminaHumanMethylation450k.db Reference Versions   Tim Triche, Jr.
• [BioC] ChIPpeakAnno, makeVennDiagram   Zhu, Lihua (Julie)
• [BioC] meta analysis   Joao Fadista
• [BioC] ChIPpeakAnno, makeVennDiagram   Zhu, Lihua (Julie)
• [BioC] problem with using GSVA package   Lapointe, David
• [BioC] problem with using GSVA package   Robert Castelo
• [BioC] problem with using GSVA package   Lapointe, David
• [BioC] problem with using GSVA package   Robert Castelo
• [BioC] problem with using GSVA package   Robert Castelo
• [BioC] remove affy probes with common SNPs   Joao Fadista
• [BioC] the procedure to annotate assembled transcriptom   wang peter
• [BioC] the procedure to annotate assembled transcriptom   Sean Davis
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Martin Morgan
• [BioC] Bioconductor, PHP, and R   hussein bazzi [guest]
• [BioC] Bioconductor, PHP, and R   Dan Tenenbaum
• [BioC] Bioconductor, PHP, and R   Dan Tenenbaum
• [BioC] Bioconductor, PHP, and R   Pierre-Yves Chibon
• [BioC] Bioconductor, PHP, and R   Hussein Hijazi
• [BioC] problem with using GSVA package   Lapointe, David
• [BioC] Bioconductor, PHP, and R   Sean Davis
• [BioC] RNAseq expression analysis using DESeq: technical replicates, paired samples   Michael Muratet
• [BioC] RNAseq expression analysis using DESeq: technical replicates, paired samples   Simon Anders
• [BioC] RNAseq expression analysis using DESeq: technical replicates, paired samples   Michael Muratet
• [BioC] Correlation analysis   Minh Bui
• [BioC] Correlation analysis   Sean Davis
• [BioC] IlluminaHumanMethylation450k.db Reference Versions   Dario Strbenac
• [BioC] Correlation analysis   Minh Bui
• [BioC] edgeR and pair-wise comparison error by estimateGLMCommonDisp   Gordon K Smyth
• [BioC] IlluminaHumanMethylation450k.db Reference Versions   Tim Triche, Jr.
• [BioC] edgeR and pair-wise comparison error by estimateGLMCommonDisp   Gordon K Smyth
• [BioC] Multiple groups comparison using EdgeR   Xiaohui Wu
• [BioC] RNAseq expression analysis using DESeq: technical replicates, paired samples   Simon Anders
• [BioC] GenomicRanges Use Cases - subsetByOverlaps   James Perkins
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Tim Rayner
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Michael Lawrence
• [BioC] Repitools/ClusterPlots   gillian [guest]
• [BioC] Correlation analysis   Sean Davis
• [BioC] Repitools/ClusterPlots   Vincent Carey
• [BioC] CRAN packages maintained by you   Kurt Hornik
• [BioC] GenomicRanges Use Cases - subsetByOverlaps   Steve Lianoglou
• [BioC] Rsamtools installation   John Coulthard
• [BioC] installation problems with goseq   Claudia Calabrese
• [BioC] Rsamtools installation   Steve Lianoglou
• [BioC] Rsamtools installation   James W. MacDonald
• [BioC] CRAN packages maintained by you   Nicholas Lewin-Koh
• [BioC] installation problems with goseq   Martin Morgan
• [BioC] Repitools/ClusterPlots   Wong, Chao-Jen
• [BioC] lumi: Methylation450 Data Input   Jiayi Sun
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Marc Carlson
• [BioC] Normalization in Coverage   Valerie Obenchain
• [BioC] how to remove redundant or error in transcripsome   wang peter
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Valerie Obenchain
• [BioC] Multiple groups comparison using EdgeR   Xiaohui Wu
• [BioC] topGO using de novo assembled transcriptome   oystercow
• [BioC] Repitools/ClusterPlots   Mark Robinson
• [BioC] installation problems with goseq   Claudia Calabrese
• [BioC] extract introns   Yating Cheng
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Tim Rayner
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Oscar Flores
• [BioC] VanillaICE   Francesco Mancuso
• [BioC] error in loading GLAD package   Qian Liu
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Hervé Pagès
• [BioC] Normalization in Coverage   rohan bareja
• [BioC] problem with frma on U133AAofAv2 platform   Wang,Ying
• [BioC] error in loading GLAD package   Martin Morgan
• [BioC] Normalization in Coverage   Valerie Obenchain
• [BioC] error in loading GLAD package   Ramon Diaz-Uriarte
• [BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?   Halian Vilela
• [BioC] visualizing genomic data   Bogdan Tanasa
• [BioC] visualizing genomic data   Tengfei Yin
• [BioC] readPileup() Error   Ron Ophir
• [BioC] Rsamtools installation   John Coulthard
• [BioC] readPileup() Error   Vincent Carey
• [BioC] Bioconductor, PHP, and R   Xavier de Pedro
• [BioC] DEseq for sample clustering   Linn Fagerberg [guest]
• [BioC] Problem installing KEGGSOAP   Paolo Sonego
• [BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?   Zhu, Lihua (Julie)
• [BioC] Rsamtools installation   Vincent Carey
• [BioC] Rsamtools installation   Vincent Carey
• [BioC] problem with frma on U133AAofAv2 platform   Matthew McCall
• [BioC] Fwd: extract introns   Steve Lianoglou
• [BioC] DESeq - read counts   Avinash S
• [BioC] extract introns   Ivan Gregoretti
• [BioC] Rsamtools installation   John Coulthard
• [BioC] topGO error, likely from topDiffGenes method of selection   Ian Mc Dowell
• [BioC] VanillaICE   Valerie Obenchain
• [BioC] VanillaICE   Robert Scharpf
• [BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?   Halian Vilela
• [BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?   Zhu, Lihua (Julie)
• [BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?   Zhu, Lihua (Julie)
• [BioC] making valid model matrix for using SNM package   Wendy Qiao
• [BioC] DESeq - read counts   Wolfgang Huber
• [BioC] DEseq for sample clustering   Wolfgang Huber
• [BioC] IlluminaHumanMethylation450k.db Reference Versions   Marc Carlson
• [BioC] visualizing genomic data   Marc Carlson
• [BioC] extract introns   Steve Lianoglou
• [BioC] extract introns   Steve Lianoglou
• [BioC] extract introns   Martin Morgan
• [BioC] extract introns   Steve Lianoglou
• [BioC] significant test when number of sample are only two???   neeraj rana
• [BioC] HTSanalyzeR GSEA Error   Dario Strbenac
• [BioC] Problems installing sva and bladderbatch   James Wagner
• [BioC] Problems installing sva and bladderbatch   Martin Morgan
• [BioC] Problems installing sva and bladderbatch   Vincent Carey
• [BioC] Problems installing sva and bladderbatch   David Iles
• [BioC] extract introns   Michael Lawrence
• [BioC] Problems installing sva and bladderbatch   James Wagner
• [BioC] readPileup() Error   Martin Morgan
• [BioC] Problems installing sva and bladderbatch   Martin Morgan
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] rsamtools installation   kevin [guest]
• [BioC] permutate data matrix   Kripa R
• [BioC] rsamtools installation   Martin Morgan
• [BioC] GSVA: using Entrez ID's as identifiers   Wendy Qiao
• [BioC] permutate data matrix   James W. MacDonald
• [BioC] permutate data matrix   Kripa R
• [BioC] design matrix limma   Reema Singh
• [BioC] design matrix limma   Sean Davis
• [BioC] readPileup() Error   Ron Ophir
• [BioC] EdgeR: Using estimateCommondisp for housekeeping genes   Tonya Mariko Brunetti
• [BioC] extract introns   Yating Cheng
• [BioC] extract introns   Yating Cheng
• [BioC] extract introns   Steve Lianoglou
• [BioC] EdgeR: Using estimateCommondisp for housekeeping genes   Mark Robinson
• [BioC] compilation error for rtracklayer   rcaloger
• [BioC] compilation error for rtracklayer   Michael Lawrence
• [BioC] [limma] Unreliable spots - omitting in avereps   mjonczyk
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Rongkun Shen [guest]
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Dan Tenenbaum
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Dan Tenenbaum
• [BioC] Sudden Issue with add for lymphGate in flowCore   Aric Gregson
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Rongkun Shen
• [BioC] compilation error for rtracklayer   Martin Morgan
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Martin Morgan
• [BioC] Sudden Issue with add for lymphGate in flowCore   Martin Morgan
• [BioC] Annotation and enrichment of a short bed list   John linux-user
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Rongkun Shen
• [BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1   Dan Tenenbaum
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Xavier de Pedro
• [BioC] rsamtools installation   Xavier de Pedro
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   john herbert
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   mjonczyk
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   Samuel Wuest
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   john herbert
• [BioC] Error while building ExpressionSet from scratch....   Bas Jansen
• [BioC] RE : rsamtools installation   Wolfgang RAFFELSBERGER
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   Mayer, Claus-Dieter
• [BioC] Error while building ExpressionSet from scratch....   Vincent Carey
• [BioC] Problem installing KEGGSOAP   Adam Rivers
• [BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering   john herbert
• [BioC] Error while building ExpressionSet from scratch....   john herbert
• [BioC] GSVA: using Entrez ID's as identifiers   Robert Castelo
• [BioC] Error while building ExpressionSet from scratch....   Martin Morgan
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Valerie Obenchain
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] Tuning segment() in DNAcopy package to get more segments on each chromosome   Qian Liu
• [BioC] Tuning segment() in DNAcopy package to get more segments on each chromosome   Sean Davis
• [BioC] Tuning segment() in DNAcopy package to get more segments on each chromosome   Qian Liu
• [BioC] EdgeR: Using estimateCommondisp for housekeeping genes   Tom Keller
• [BioC] Genentech Summer Internship Program 2012   Hsin-Ju Hsieh
• [BioC] GSVA: using Entrez ID's as identifiers   Wendy Qiao
• [BioC] Adding Multiple quadrantGates of Same Channels to workFlow (flowCore)   Aric Gregson
• [BioC] convert GeneSetCollection to a list   Wendy Qiao
• [BioC] GSVA: using Entrez ID's as identifiers   Robert Castelo
• [BioC] convert GeneSetCollection to a list   Robert Castelo
• [BioC] Error while building ExpressionSet from scratch....   Bas Jansen
• [BioC] Addition of Orangutan genome to BSgenomes   Colm Nestor
• [BioC] Possible bug in SNPchip   Francesco Mancuso
• [BioC] extract introns   Yating Cheng
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] Adding Multiple quadrantGates of Same Channels to workFlow (flowCore)   Aric Gregson
• [BioC] extract introns   Steve Lianoglou
• [BioC] extract introns   Yating Cheng
• [BioC] GSVA: using Entrez ID's as identifiers   Tom Keller
• [BioC] extract introns   Steve Lianoglou
• [BioC] extract introns   Yating Cheng
• [BioC] Augmenting metadata values in GRanges object   Fahim Mohammad
• [BioC] Augmenting metadata values in GRanges object   Martin Morgan
• [BioC] Augmenting metadata values in GRanges object   Martin Morgan
• [BioC] extract introns   Michael Lawrence
• [BioC] extract introns   Steve Lianoglou
• [BioC] readCelFile function in Starr is crashing R   Noah Dowell [guest]
• [BioC] Augmenting metadata values in GRanges object   Fahim Mohammad
• [BioC] RE : rsamtools installation   Martin Morgan
• [BioC] PhD position available in Innsbruck, Austria   Johannes Rainer
• [BioC] GSVA: using Entrez ID's as identifiers   Robert Castelo
• [BioC] bayseq and edgeR for multi groups comparisons   lpascual
• [BioC] subsetting IntegerList by list names   Manuela Hummel
• [BioC] readCelFile function in Starr is crashing R   Kasper Daniel Hansen
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Steffen Durinck
• [BioC] subsetting IntegerList by list names   Martin Morgan
• [BioC] subsetting IntegerList by list names   Steve Lianoglou
• [BioC] extract introns   Yating Cheng
• [BioC] subsetting IntegerList by list names   Martin Morgan
• [BioC] readCelFile function in Starr is crashing R   Noah Dowell
• [BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?   Adriana Munoz
• [BioC] GSVA: using Entrez ID's as identifiers   Robert Castelo
• [BioC] bayseq and edgeR for multi groups comparisons   Gordon K Smyth
• [BioC] GSVA: using Entrez ID's as identifiers   Marc Carlson
• [BioC] possible bug in ShortRead qa/ppnCount   Janet Young
• [BioC] Possible bug in SNPchip   Robert Scharpf
• [BioC] subsetting IntegerList by list names   Tom Keller
• [BioC] Using proportions...   Jim Silverton
• [BioC] package Genominator with ShortRead-annotation question   nitzan kol [guest]
• [BioC] PhD position available in Innsbruck, Austria   Johannes Rainer
• [BioC] problem using affxparser on MacOSX   Fabrice Berger
• [BioC] problem using affxparser on MacOSX   Sean Davis
• [BioC] problem using affxparser on MacOSX   Fabrice Berger
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Stefanie Ververs
• [BioC] DESeq Error: pobs == ps[kAs[i] + 1] is not TRUE   Robert Castelo
• [BioC] GSVA: using Entrez ID's as identifiers   somnath bandyopadhyay
• [BioC] Using proportions...   Wolfgang Huber
• [BioC] Using proportions...   Wolfgang Huber
• [BioC] TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq   Smith, Hilary A
• [BioC] TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq   Wolfgang Huber
• [BioC] problem using affxparser on MacOSX   Noah Dowell
• [BioC] HTSanalyzeR GSEA Error   Xin Wang
• [BioC] problem using affxparser on MacOSX   Noah Dowell
• [BioC] Rgraphviz produces segmentation fault when attempting to plot Bayesian Belief Networks   Royce Francis
• [BioC] Rgraphviz produces segmentation fault when attempting to plot Bayesian Belief Networks   Sean Davis
• [BioC] Rgraphviz produces segmentation fault when attempting to plot Bayesian Belief Networks   Royce Francis
• [BioC] GSVA: using Entrez ID's as identifiers   Robert Castelo
• [BioC] possible bug in ShortRead qa/ppnCount   Martin Morgan
• [BioC] permutation loop   Kripa R
• [BioC] GSVA: using Entrez ID's as identifiers   somnath bandyopadhyay
• [BioC] diagnosing problems with processing microarray data using lumi package   Juliet Hannah
• [BioC] permutation loop   Achilleas Pitsillides
• [BioC] GRanges - reduce() function   Fahim Mohammad
• [BioC] package Genominator with ShortRead-annotation question   Kasper Daniel Hansen
• [BioC] subsetting IntegerList by list names   Hervé Pagès
• [BioC] HTSanalyzeR GSEA Error   Dario Strbenac
• [BioC] GRanges - reduce() function   Jason Ross
• [BioC] GRanges - reduce() function   Vincent Carey
• [BioC] edgeR: exactTest different p value in new version 2.4   Sermsawat Tunlaya-anukit
• [BioC] edgeR: exactTest different p value in new version 2.4   Gordon K Smyth
• [BioC] edgeR: exactTest different p value in new version 2.4   Gordon K Smyth
• [BioC] RE : RE : rsamtools installation   Wolfgang RAFFELSBERGER
• [BioC] RE : RE : rsamtools installation   Martin Morgan
• [BioC] GRanges - reduce() function   Martin Morgan
• [BioC] finding out which tags are in a bam-file   Hubert Rehrauer
• [BioC] GRanges - reduce() function   Kasper Daniel Hansen
• [BioC] \"normalize a subset of affy data\" AND \"R help function\"   Anup Som [guest]
• [BioC] GRanges - reduce() function   Fahim Mohammad
• [BioC] Addition of Orangutan genome to BSgenomes   Valerie Obenchain
• [BioC] TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)   Thomas J Hardcastle
• [BioC] \"normalize a subset of affy data\" AND \"R help function\"   mjonczyk
• [BioC] GRanges - reduce() function   Hervé Pagès
• [BioC] GRanges - reduce() function   Cook, Malcolm
• [BioC] edgeR   Bogdan Tanasa
• [BioC] GRanges - reduce() function   Hervé Pagès
• [BioC] edgeR   Mark Robinson
• [BioC] Problem installing KEGGSOAP   Dan Tenenbaum
• [BioC] KEGGSOAP incomplete list.pathways   kevin [guest]
• [BioC] gaoshan   wang peter
• [BioC] finding out which tags are in a bam-file   Martin Morgan
• [BioC] gaoshan   Martin Morgan
• [BioC] GRanges - reduce() function   Fahim Mohammad
• [BioC] installing gtk for EBImage   Ravi [guest]
• [BioC] extract introns   Hervé Pagès
• [BioC] edgeR   Bogdan Tanasa
• [BioC] KEGGSOAP incomplete list.pathways   Marc Carlson
• [BioC] package NEWS, README, and INSTALL files available on web site   Dan Tenenbaum
• [BioC] TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq   Gordon K Smyth
• [BioC] TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq   Smith, Hilary A
• [BioC] seqSegment readGeneric() function error   jiayu wen
• [BioC] seqSegment readGeneric() function error   Martin Morgan
• [BioC] DESeq Error: pobs == ps[kAs[i] + 1] is not TRUE   Simon Anders
• [BioC] GSVA error when trying to bootstrap   somnath bandyopadhyay
• [BioC] edgeR   Bogdan Tanasa
• [BioC] Error in doing QC for 450K IlluminaHumanMeth data using methylumi   Shruti Rastogi
• [BioC] Limma question: readGenericHeader error message   Ella Chang
• [BioC] Chemometrics Analysis   Andre Dejam
• [BioC] GSVA error when trying to bootstrap   Justin Guinney
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] problem with GO terms   James W. MacDonald
• [BioC] export Views of Rle in rtracklayer   Jason Lu
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] problem with GO terms   James W. MacDonald
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] retrieve the level for a GO category   Biase, Fernando Henrique
• [BioC] edgeR: what to do with no replicates   Gordon K Smyth
• [BioC] edgeR: what to do with no replicates   Bogdan Tanasa
• [BioC] edgeR: what to do with no replicates   Gordon K Smyth
• [BioC] Limma question: readGenericHeader error message   Gordon K Smyth
• [BioC] export Views of Rle in rtracklayer   Martin Morgan
• [BioC] edgeR: what to do with no replicates   Bogdan Tanasa
• [BioC] retrieve the level for a GO category   Martin Morgan
• [BioC] which statistical test to perform?   anand mt [guest]
• [BioC] retrieve the level for a GO category   Vincent Carey
• [BioC] which statistical test to perform?   Sean Davis
• [BioC] which statistical test to perform?   Sean Davis
• [BioC] Affy U133 array CEL files - how can i see individual probe signals?   Deb [guest]
• [BioC] NucleR: processReads/solveUserSEW0 - Error   Oscar Flores
• [BioC] Affy U133 array CEL files - how can i see individual probe signals?   Sean Davis
• [BioC] which statistical test to perform?   anand m t
• [BioC] export Views of Rle in rtracklayer   Michael Lawrence
• [BioC] which statistical test to perform?   Richard Friedman
• [BioC] export Views of Rle in rtracklayer   Jason Lu
• [BioC] compilation error for rtracklayer   Michael Lawrence
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Karl Brand
• [BioC] export Views of Rle in rtracklayer   Michael Lawrence
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Dan Tenenbaum
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   James W. MacDonald
• [BioC] export Views of Rle in rtracklayer   Jason Lu
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Martin Morgan
• [BioC] selecting/filtering probesets from exprSet object prior to diff. exp. anal.   Mark Baumeister
• [BioC] selecting/filtering probesets from exprSet object prior to diff. exp. anal.   James W. MacDonald
• [BioC] Using Rscript to run DEXSeq on Linux cluster   Christopher T Gregg
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Iain Gallagher
• [BioC] selecting/filtering probesets from exprSet object prior to diff. exp. anal.   Mark Baumeister
• [BioC] selecting/filtering probesets from exprSet object prior to diff. exp. anal.   James W. MacDonald
• [BioC] Some more rtracklayer questions (re: WIG and .VSTEP files)   Tim Triche, Jr.
• [BioC] Using Rscript to run DEXSeq on Linux cluster   Steve Lianoglou
• [BioC] Some more rtracklayer questions (re: WIG and .VSTEP files)   Michael Lawrence
• [BioC] export Views of Rle in rtracklayer   Michael Lawrence
• [BioC] Some more rtracklayer questions (re: WIG and .VSTEP files)   Tim Triche, Jr.
• [BioC] GRanges - reduce() function   Michael Lawrence
• [BioC] export Views of Rle in rtracklayer   Jason Lu
• [BioC] Plot Multiple 'Backgates' Simultaneously flowViz   Aric Gregson
• [BioC] DESeq adjusted pvalue calculation / filtering data   Markus Grohme
• [BioC] Bioconductor does not install properly   Bas Jansen
• [BioC] Bioconductor does not install properly   Vincent Carey
• [BioC] Bioconductor does not install properly   Benilton Carvalho
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Karl Brand
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Karl Brand
• [BioC] Bioconductor does not install properly   Bas Jansen
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Mike Smith
• [BioC] SOLVED Re: Bioconductor does not install properly   Bas Jansen
• [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)   Karl Brand
• [BioC] biostrints translate() ambiguities?   James Walters [guest]
• [BioC] Fwd: Bioconductor does not install properly   Dan Tenenbaum
• [BioC] Some more rtracklayer questions (re: WIG and .VSTEP files)   Michael Lawrence
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Firas Swidan
• [BioC] PFAM gene enrichment test using GOstats and Category   Henrik De Fine Licht
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Vincent Carey
• [BioC] DESeq adjusted pvalue calculation / filtering data   Simon Anders
• [BioC] solution for affy human 500k mapping snp array   Xiaokuan Wei
• [BioC] solution for affy human 500k mapping snp array   Vincent Carey
• [BioC] GRanges - reduce() function   Michael Lawrence
• [BioC] GRanges - coercion from dataframe   Fahim Mohammad
• [BioC] custom SNPlocs / BSgenome package   km
• [BioC] DESeq adjusted pvalue calculation / filtering data   Naomi Altman
• [BioC] solution for affy human 500k mapping snp array   Xiaokuan Wei
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Dan Tenenbaum
• [BioC] GRanges - coercion from dataframe   Fahim Mohammad
• [BioC] solution for affy human 500k mapping snp array   Benilton Carvalho
• [BioC] GRanges - coercion from dataframe   Michael Lawrence
• [BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"   Mikhail Spivakov [guest]
• [BioC] HTqPCR and Biobase's eSet   Laurent Gautier
• [BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"   Vincent Carey
• [BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"   Mikhail Spivakov
• [BioC] custom SNPlocs / BSgenome package   Valerie Obenchain
• [BioC] GRanges - coercion from dataframe   Steve Lianoglou
• [BioC] Using Rscript to run DEXSeq on Linux cluster   Wolfgang Huber
• [BioC] Block x Treatment interaction test with DeSeq   Miguel Gallach
• [BioC] Analysis with SnpSet object CRLMM package   Chintan Vora - Xcelris
• [BioC] density plot of pm values   Assa Yeroslaviz
• [BioC] Block x Treatment interaction test with DeSeq   Simon Anders
• [BioC] sub-setting arrays   Assa Yeroslaviz
• [BioC] sub-setting arrays   Heidi Dvinge
• [BioC] sub-setting arrays   Vincent Carey
• [BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"   audrey kauffmann
• [BioC] GRanges - coercion from dataframe   Kasper Daniel Hansen
• [BioC] edgeR - R script - results compared to DESeq   Avinash S
• [BioC] edgeR - R script - results compared to DESeq   Avinash S
• [BioC] edgeR - R script - results compared to DESeq   Avinash S
• [BioC] density plot of pm values   James W. MacDonald
• [BioC] edgeR - R script - results compared to DESeq   Simon Anders
• [BioC] installation of bioconductopr packages fails   Ina Hoeschele
• [BioC] installation of bioconductopr packages fails   Kasper Daniel Hansen
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] problem with GO terms   James W. MacDonald
• [BioC] goseq problem   Christopher T Gregg
• [BioC] goseq problem   Christopher T Gregg
• [BioC] HTqPCR and Biobase's eSet   James Perkins
• [BioC] Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   andrea.grilli at ior.it
• [BioC] gwSnpTests in GGtools   francy [guest]
• [BioC] DESeq adjusted pvalue calculation / filtering data   Markus Grohme
• [BioC] intragenic sequence extraction   Yating Cheng
• [BioC] gwSnpTests in GGtools   Vincent Carey
• [BioC] intragenic sequence extraction   Steve Lianoglou
• [BioC] edgeR on differentially expressed genes with low read counts   Lucía [guest]
• [BioC] Analysis with SnpSet object CRLMM package   Benilton Carvalho
• [BioC] error in DEXSeq fitDispersionFunction()   Georg Otto
• [BioC] gwSnpTests in GGtools   francesca casalino
• [BioC] Limma Dual Color Agilent : Mixed model or not ?   Guillaume Meurice
• [BioC] gwSnpTests in GGtools   Vincent Carey
• [BioC] Need help for designing microarray experiment   Christian Brière
• [BioC] PFAM gene enrichment test using GOstats and Category   Marc Carlson
• [BioC] density plot of pm values   Naomi Altman
• [BioC] DESeq adjusted pvalue calculation / filtering data   Naomi Altman
• [BioC] fasta sequence is too long to be read   wang peter
• [BioC] edgeR on differentially expressed genes with low read counts   Naomi Altman
• [BioC] problem with GO terms   Marc Carlson
• [BioC] edgeR on differentially expressed genes with low read counts   Simon Anders
• [BioC] fasta sequence is too long to be read   Steve Lianoglou
• [BioC] DESeq gene names under id   Mary Ann Allen
• [BioC] Using GTF gene annotation to build a GemomicRanges Object   sunny [guest]
• [BioC] problem with GO terms   Ina Hoeschele
• [BioC] Using GTF gene annotation to build a GemomicRanges Object   Vincent Carey
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Firas Swidan
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Dan Tenenbaum
• [BioC] help on limma design for the agilent microarray   Ella Chang
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Firas Swidan
• [BioC] Using GTF gene annotation to build a GemomicRanges Object   Sunny Yu Liu
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Dan Tenenbaum
• [BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script   Firas Swidan
• [BioC] DESeq gene names under id   Simon Anders
• [BioC] edgeR - R script - results compared to DESeq   Gordon K Smyth
• [BioC] Using GTF gene annotation to build a GemomicRanges Object   Michael Lawrence
• [BioC] Using GTF gene annotation to build a GemomicRanges Object   Sunny Yu Liu
• [BioC] edgeR on differentially expressed genes with low read counts   Gordon K Smyth
• [BioC] Inconsistency in illuminaHumanv4.db ?   Holger [guest]
• [BioC] GRanges - reduce() function   Jason Ross
• [BioC] GRanges - reduce() function   Michael Lawrence
• [BioC] Analysis with SnpSet object CRLMM package   Chintan Vora - Xcelris
• [BioC] edgeR on differentially expressed genes with low read counts   Gordon K Smyth
• [BioC] some basic questions   anand mt [guest]
• [BioC] Probe level normalization   suri ghani
• [BioC] gwSnpTests in GGtools   francesca casalino
• [BioC] edgeR - R script - results compared to DESeq   Smith, Hilary A
• [BioC] Limma warnings and how to extract normalized CY5, CY3 intensities   asas asasa
• [BioC] Limma warnings and how to extract normalized CY5, CY3 intensities   Christian Brière
• [BioC] some basic questions   Richard Friedman
• [BioC] some basic questions   Sean Davis
• [BioC] Probe level normalization   James W. MacDonald
• [BioC] Probe level normalization   wang peter
• [BioC] Maximal length of Rle vectors   Hans-Ulrich Klein
• [BioC] issue with limma?   Kripa R
• [BioC] issue with limma?   Wei Shi
• [BioC] issue with limma?   Sean Davis
• [BioC] Maximal length of Rle vectors   Hervé Pagès

Last message date: Wed Nov 30 23:53:07 CET 2011
Archived on: Thu Dec 1 13:03:11 CET 2011

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