January 2013 Archives by author

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Starting: Tue Jan 1 11:59:54 CET 2013
Ending: Thu Jan 31 23:24:07 CET 2013
Messages: 698

• [BioC] BeadArray   Gaye SAGINC (GIS)
• [BioC] Conference Announcement - CAMDA 2013   CAMDA 2013
• [BioC] topGO quick start guide error   Fix Ace
• [BioC] topGO quick start guide error   Fix Ace
• [BioC] question about "evidence cole" in data.frame from GOstats packages with unsupported model organisms   Fix Ace
• [BioC] question about "evidence code" in data.frame from GOstats packages with unsupported model organisms   Fix Ace
• [BioC] question about "evidence code" in data.frame from GOstats packages with unsupported model organisms (Marc Carlson)   Fix Ace
• [BioC] Difficulties in using the mgsa package for Gene Set Analysis   Adrian Segarra, Juan
• [BioC] GLM in DEseq   Simon Anders
• [BioC] DESeq - working with more than 2 conditions   Simon Anders
• [BioC] DEXSeq: problem with dexseq_prepare_annotation.py   Simon Anders
• [BioC] Installing packages   Andrés
• [BioC] [methylumi] concerning methylumi.bgcorr function and out-of-band intensities   Dylan Aïssi
• [BioC] Difficulties in using the mgsa package for Gene Set Analysis   Sebastian Bauer
• [BioC] rtracklayer: small problem   Gustavo Fernández Bayón
• [BioC] rtracklayer: small problem   Gustavo Fernández Bayón
• [BioC] rhdf5 and factors   Moritz Emanuel Beber
• [BioC] Limma Voom R package   Pedro Blecua
• [BioC] log transform in RMA normalization   Benjamin Bolstad
• [BioC] biomaRt does not load archived Ensembl Genes database anymore.   J.H. Brandsma
• [BioC] biomaRt does not load archived Ensembl Genes database anymore.   J.H. Brandsma
• [BioC] DiffBind error   Gordon Brown
• [BioC] Nucleotide percentages?   Caitlin
• [BioC] mm10 goseq supported genome   Vincenzo Capece
• [BioC] DEXSeq: building exon count set   Vincenzo Capece
• [BioC] DEXSeq: building exon count set   Vincenzo Capece
• [BioC] Bioconductor Cloud AMI   Vincent Carey
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Vincent Carey
• [BioC] snpStats --- MAF in Pedigrees   Vincent Carey
• [BioC] getGEO error   Vincent Carey
• [BioC] Gene Ontology: Shortest path from root to node   Marc Carlson
• [BioC] Gene Ontology: Shortest path from root to node   Marc Carlson
• [BioC] Gene Ontology: Shortest path from root to node   Marc Carlson
• [BioC] question about "evidence code" in data.frame from GOstats packages with unsupported model organisms   Marc Carlson
• [BioC] Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands   Marc Carlson
• [BioC] question about "evidence code" in data.frame from GOstats packages with unsupported model organisms (Marc Carlson)   Marc Carlson
• [BioC] DEXSeq package - read.HTSeqCount function error   Matteo Carrara
• [BioC] Oligo - oligo::probeNames() returns transcript clusters, not probe sets   Benilton Carvalho
• [BioC] BSgenome forging - Node stack overflow   Sara Castelletti
• [BioC] BSgenome forging - Node stack overflow   Sara Castelletti
• [BioC] parallel and GSVA   Robert Castelo
• [BioC] parallel and GSVA   Robert Castelo
• [BioC] [GSVA] Segfault with GSVA   Robert Castelo
• [BioC] [PATCH] Fix options in GSVA   Robert Castelo
• [BioC] Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package   Christina Chaivorapol
• [BioC] Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x   Christina Chaivorapol
• [BioC] Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x   Christina Chaivorapol
• [BioC] Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs   Fong Chun Chan
• [BioC] Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs   Fong Chun Chan
• [BioC] Efficiently running DEXSeq for Large Cohorts   Fong Chun Chan
• [BioC] Efficiently running DEXSeq for Large Cohorts   Fong Chun Chan
• [BioC] Efficiently running DEXSeq for Large Cohorts   Fong Chun Chan
• [BioC] Efficiently running DEXSeq for Large Cohorts   Fong Chun Chan
• [BioC] Efficiently running DEXSeq for Large Cohorts   Fong Chun Chan
• [BioC] Getting Introns Expression at a Per Gene Level   Fong Chun Chan
• [BioC] Limma and XML   Chen, Wei
• [BioC] Limma and XML   Chen, Wei
• [BioC] Problem with biomaRt update in R-2.15.1   Eleni Christodoulou
• [BioC] Can we use DNAcopy to analyse Copy Number Viaration using next generation sequencing data generated by eigher Ion PGM or Illumina MiSeq   Djork-Arné Clevert
• [BioC] countMatches() (was: table for GenomicRanges)   Cook, Malcolm
• [BioC] countMatches() (was: table for GenomicRanges)   Cook, Malcolm
• [BioC] countMatches() (was: table for GenomicRanges)   Cook, Malcolm
• [BioC] countMatches() (was: table for GenomicRanges)   Cook, Malcolm
• [BioC] subset GRanges   Cook, Malcolm
• [BioC] new package for generating interactive HTML reports   Cook, Malcolm
• [BioC] new package for generating interactive HTML reports   Cook, Malcolm
• [BioC] emacs org mode html export using jQuery DataTables (WAS: new package for generating interactive HTML reports)   Cook, Malcolm
• [BioC] Using fRMA with "alternative" CDF files   Cornwell, Adam
• [BioC] Using fRMA with "alternative" CDF files   Cornwell, Adam
• [BioC] Comparing human and mouse expression directly with RankProd   Cornwell, Adam
• [BioC] flowCore log transformation   Pieter Coussement
• [BioC] FlowCore - read.flowSet   Pieter Coussement
• [BioC] FlowCore - reading in flowSets   Pieter Coussement
• [BioC] strategy to match/align peptide sequence to protein   Philippe DESSEN
• [BioC] Problems with mapping chromosomal probe locations for illumina probes ?!   Philippe DESSEN
• [BioC] mm10 goseq supported genome   Nadia Davidson
• [BioC] countMatches() (was: table for GenomicRanges)   Sean Davis
• [BioC] GEOquery getGEO error in read.table   Sean Davis
• [BioC] new package for generating interactive HTML reports   Sean Davis
• [BioC] new package for generating interactive HTML reports   Sean Davis
• [BioC] Basic ExpressionSet problems   Sean Davis
• [BioC] methyAnalysis methyGenoSet function   Sean Davis
• [BioC] reading data in AgiMicroRna package   Sean Davis
• [BioC] is it possible to find sample batch # in CEL files?   Sean Davis
• [BioC] getGEO error   Sean Davis
• [BioC] bioc data set not found   Sean Davis
• [BioC] getGEO error   Sean Davis
• [BioC] Meaning of Median and IQR in MA-Plot, Affy Package   Sean Davis
• [BioC] easyRNAseq remove overlapping features   Nicolas Delhomme
• [BioC] vsn preprocess with oligo package   Nicolas Delhomme
• [BioC] using easyRNASeq to calculate RPKM values   Nicolas Delhomme
• [BioC] Error when splitting an AAStringSet   Nicolas Delhomme
• [BioC] Error when splitting an AAStringSet   Nicolas Delhomme
• [BioC] Problems in running easyRNASeq   Nicolas Delhomme
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Darwin Sorento Dichmann
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Darwin Sorento Dichmann
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Darwin Sorento Dichmann
• [BioC] importing data problem with methyAnalysis package   Pan Du
• [BioC] Loading Data into MethyAnalysis   Pan Du
• [BioC] Variability Plot For Toray Microarray Data   Peverall Dubois
• [BioC] ggsave option for ggbio Tracks function   Mark Dunning
• [BioC] ggsave option for ggbio Tracks function   Mark Dunning
• [BioC] BeadArray   Mark Dunning
• [BioC] get pixel coordinates interactively with EBimage   Arnaud Duranel
• [BioC] getSequence from biomaRt changes the order of sequences given as input - is it normal?   Steffen Durinck
• [BioC] biomaRt does not load archived Ensembl Genes database anymore.   Steffen Durinck
• [BioC] biomaRt query: retrieve exon locations etc   Steffen Durinck
• [BioC] BiomaRt: getLDS keeps returning NULL   Steffen Durinck
• [BioC] affy code archeology: expresso behavior for liwong/invariantset   David Eby
• [BioC] GeneFeatureSet   Shahenda El-Naggar
• [BioC] Bioconductor Cloud AMI   Rohmatul Fajriyah
• [BioC] Bioconductor Cloud AMI   Rohmatul Fajriyah
• [BioC] Bioconductor Cloud AMI   Rohmatul Fajriyah
• [BioC] DESeq package error   Fares Z. Najar, Ph.D.
• [BioC] DESeq package error   Fares Z. Najar, Ph.D.
• [BioC] DESeq package error   Fares Z. Najar, Ph.D.
• [BioC] Error installing iFlow (Jaques Fattaccioli)   Finak, Greg
• [BioC] rhdf5 and factors   Bernd Fischer
• [BioC] rhdf5 and factors   Bernd Fischer
• [BioC] Basic ExpressionSet problems   Forst, Christian
• [BioC] ExpressionSet Time-series correlation stuff   Forst, Christian
• [BioC] ExpressionSet Time-series correlation stuff   Forst, Christian
• [BioC] ExpressionSet Time-series correlation stuff   Forst, Christian
• [BioC] AffylmGUI freezes with recent updates of Windows 7 Enterprise Service Pack 1   Richard Friedman
• [BioC] Methods for time course gene expression analysis in an observational cohort   Richard Friedman
• [BioC] Methods for time course gene expression analysis in an observational cohort   Richard Friedman
• [BioC] statistical test for time course data   Richard Friedman
• [BioC] significance of correlation genes/miRNAs expression   Paul Geeleher
• [BioC] Post-doc position available   Robert Gentleman
• [BioC] BitSeq: Required input for 3' bias correction on transcripts.   Dave Gerrard
• [BioC] BitSeq: Required input for 3' bias correction on transcripts.   Dave Gerrard
• [BioC] methyAnalysis methyGenoSet function   Giancarlo
• [BioC] Bioinformatics Position Opening   Thomas Girke
• [BioC] BitSeq: Required input for 3' bias correction on transcripts.   Peter Glaus
• [BioC] merging VCF files   Stephanie M. Gogarten
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   Stephanie M. Gogarten
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Lavinia Gordon
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Lavinia Gordon
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Lavinia Gordon
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Lavinia Gordon
• [BioC] Problems with mapping chromosomal probe locations for illumina probes ?!   Fenton Christopher Graham
• [BioC] Finding a amino acid regular expression pattern in a beta sheet?   Fenton Christopher Graham
• [BioC] xps: hugene11 chip gives problems   Groot, Philip de
• [BioC] xps: hugene11 chip gives problems   Groot, Philip de
• [BioC] Data analyst job at Novartis   Hahne, Florian
• [BioC] question regarding gviz   Hahne, Florian
• [BioC] Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands   Hahne, Florian
• [BioC] strategy to match/align peptide sequence to protein   Juliet Hannah
• [BioC] Log transformation and left censoring   Paul Harrison
• [BioC] Fwd: problem RangedData   Silvia von der Heyde
• [BioC] problem RangedData   Silvia von der Heyde
• [BioC] Methods for time course gene expression analysis in an observational cohort   Oliver Hofmann
• [BioC] Methods for time course gene expression analysis in an observational cohort   Oliver Hofmann
• [BioC] Methods for time course gene expression analysis in an observational cohort   Oliver Hofmann
• [BioC] is it possible to find sample batch # in CEL files?   Hooiveld, Guido
• [BioC] KEGG REST: retrieving genes   Hooiveld, Guido
• [BioC] KEGG REST: retrieving genes   Hooiveld, Guido
• [BioC] error message relating to png file when running maQualityPlots   Yanqing Hu
• [BioC] Problem with biomaRt update in R-2.15.1   Wolfgang Huber
• [BioC] is it possible to find sample batch # in CEL files?   Wolfgang Huber
• [BioC] rhdf5 and factors   Wolfgang Huber
• [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname   Toby Hughes
• [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname   Toby Hughes
• [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname   Toby Hughes
• [BioC] GSEABase error parsing msigdb_v3.1.xml   Lina Hultin-Rosenberg
• [BioC] GSEABase error parsing msigdb_v3.1.xml   Lina Hultin-Rosenberg
• [BioC] new package for generating interactive HTML reports   Melanie Huntley
• [BioC] new package for generating interactive HTML reports   Melanie Huntley
• [BioC] Empty Granges   Marco Lo Iacono
• [BioC] parallel and GSVA   David Iles
• [BioC] parallel and GSVA   David Iles
• [BioC] parallel and GSVA   David Iles
• [BioC] ComBat   Gayatri Iyer
• [BioC] ComBat   Gayatri Iyer
• [BioC] statistical test for time course data   chris Jhon
• [BioC] time series expression data   Adrian Johnson
• [BioC] about ComBat plot for non parametric   Johnson, William Evan
• [BioC] Windows or Excel to R txt file   Maciej Jończyk
• [BioC] Query regarding limma   Maciej Jończyk
• [BioC] Double KO and timecourse design / limma   Textoris Julien
• [BioC] Double KO and timecourse design / limma   Textoris Julien
• [BioC] GEOquery getGEO error in read.table   Textoris Julien
• [BioC] new package for generating interactive HTML reports   Josh Kaminker
• [BioC] edgeR continuous variables   Fredrik Karlsson
• [BioC] AffylmGUI freezes with recent updates of Windows 7 Enterprise Service Pack 1   Keith
• [BioC] subset GRanges   Wim Kreinen
• [BioC] subset GRanges   Wim Kreinen
• [BioC] Bioconductor Digest, Vol 119, Issue 1   Leo Lahti
• [BioC] Problem in KEGGSOAP package   Asta Laiho
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] status of visnab   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] Turning a GRanges Metadata Column into Rle List   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] Turning a GRanges Metadata Column into Rle List   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] countMatches() (was: table for GenomicRanges)   Michael Lawrence
• [BioC] reducing hits from countGenomicOverlaps()   Michael Lawrence
• [BioC] rtracklayer export method requires unique names   Michael Lawrence
• [BioC] ggbio : misplaced tracks in a test case   Michael Lawrence
• [BioC] Using GenomicRanges with table data   Michael Lawrence
• [BioC] new package for generating interactive HTML reports   Michael Lawrence
• [BioC] new package for generating interactive HTML reports   Michael Lawrence
• [BioC] rtracklayer: small problem   Michael Lawrence
• [BioC] Open computational biologist position at Genentech   Michael Lawrence
• [BioC] Class for a DataFrame of Matrices   Michael Lawrence
• [BioC] Class for a DataFrame of Matrices   Michael Lawrence
• [BioC] problem RangedData   Michael Lawrence
• [BioC] problem RangedData   Michael Lawrence
• [BioC] SNPlocs -> VCF or similar   Michael Lawrence
• [BioC] Error in Installing BioBase Development version   Paul Leo
• [BioC] seqlevels in VCF objects   Paul Leo
• [BioC] Turning a GRanges Metadata Column into Rle List   Paul Leo
• [BioC] Turning a GRanges Metadata Column into Rle List   Paul Leo
• [BioC] R 2.15.2 trouble   Paul Leo
• [BioC] getSequence from biomaRt changes the order of sequences given as input - is it normal?   Emmanuel Levy
• [BioC] getSequence from biomaRt changes the order of sequences given as input - is it normal?   Emmanuel Levy
• [BioC] Computer for the analysis of high-throughput genomic data   Steve Lianoglou
• [BioC] need help regarding quality assessment of raw data   Steve Lianoglou
• [BioC] need help regarding quality assessment of raw data   Steve Lianoglou
• [BioC] need help regarding quality assessment of raw data   Steve Lianoglou
• [BioC] DESeq package error   Steve Lianoglou
• [BioC] subset GRanges   Steve Lianoglou
• [BioC] Limma and XML   Steve Lianoglou
• [BioC] new package for generating interactive HTML reports   Steve Lianoglou
• [BioC] parallel and GSVA   Steve Lianoglou
• [BioC] Using GenomicRanges with table data   Steve Lianoglou
• [BioC] Limma and XML   Steve Lianoglou
• [BioC] Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs   Steve Lianoglou
• [BioC] Nucleotide percentages?   Steve Lianoglou
• [BioC] Efficiently running DEXSeq for Large Cohorts   Steve Lianoglou
• [BioC] BAM files to Genomic Ranges object   Steve Lianoglou
• [BioC] BAM files to Genomic Ranges object   Steve Lianoglou
• [BioC] error installing KEGGSOAP   Steve Lianoglou
• [BioC] BAM files to Genomic Ranges object   Steve Lianoglou
• [BioC] BAM files to Genomic Ranges object   Steve Lianoglou
• [BioC] differential expression analysis for 1 vs 1 experiment   Steve Lianoglou
• [BioC] Normalization   Steve Lianoglou
• [BioC] DEXSeq estimating dispersions and multiple conditions   Steve Lianoglou
• [BioC] Variability Plot For Toray Microarray Data   Steve Lianoglou
• [BioC] how to understand the concept metadata in bioconductor   Steve Lianoglou
• [BioC] how to understand the concept metadata in bioconductor   Steve Lianoglou
• [BioC] how to understand the concept metadata in bioconductor   Steve Lianoglou
• [BioC] mm10 goseq supported genome   Steve Lianoglou
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   Steve Lianoglou
• [BioC] Variability Plot For Toray Microarray Data   Steve Lianoglou
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   Steve Lianoglou
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   Steve Lianoglou
• [BioC] LogFC query in Limma   Steve Lianoglou
• [BioC] LogFC query in Limma   Steve Lianoglou
• [BioC] geneid to gene name conversion   Matthew Liebers
• [BioC] edgeR version   KJ Lim
• [BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp   KJ Lim
• [BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp   KJ Lim
• [BioC] question of justRMA on exon array   Jack Luo
• [BioC] question of justRMA on exon array   Jack Luo
• [BioC] xps installation question   Jack Luo
• [BioC] log transform in RMA normalization   Jack Luo
• [BioC] vsn preprocess with oligo package   José LÓPEZ
• [BioC] vsn preprocess with oligo package   José LÓPEZ
• [BioC] vsn preprocess with oligo package   José LÓPEZ
• [BioC] vsn preprocess with oligo package   José LÓPEZ
• [BioC] vsn preprocess with oligo package   José López
• [BioC] error message relating to png file when running maQualityPlots   James W. MacDonald
• [BioC] GeneFeatureSet   James W. MacDonald
• [BioC] Problem with biomaRt update in R-2.15.1   James W. MacDonald
• [BioC] Limma Voom R package   James W. MacDonald
• [BioC] Problems with 'affxparser' package   James W. MacDonald
• [BioC] Problems with 'affxparser' package   James W. MacDonald
• [BioC] Error installing iFlow   James W. MacDonald
• [BioC] topGO quick start guide error   James W. MacDonald
• [BioC] Nimblegen arrays; random probes   James W. MacDonald
• [BioC] vsn preprocess with oligo package   James W. MacDonald
• [BioC] vsn preprocess with oligo package   James W. MacDonald
• [BioC] vsn preprocess with oligo package   James W. MacDonald
• [BioC] Filtering out duplicate probes in Affy data   James W. MacDonald
• [BioC] phenoTest and variable-wise multiple testing   James W. MacDonald
• [BioC] Filtering out duplicate probes in Affy data   James W. MacDonald
• [BioC] question of justRMA on exon array   James W. MacDonald
• [BioC] paper - download - pubmed   James W. MacDonald
• [BioC] ‘AnnotationForge’ is not available for Linux system??   James W. MacDonald
• [BioC] affy annotation database   James W. MacDonald
• [BioC] ExpressionSet Time-series correlation stuff   James W. MacDonald
• [BioC] ExpressionSet Time-series correlation stuff   James W. MacDonald
• [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?   James W. MacDonald
• [BioC] R error by installing the org.Hs.eg.db package   James W. MacDonald
• [BioC] annotations   James W. MacDonald
• [BioC] Error message (probably) from AffyBatch.R when using a modified CDF   James W. MacDonald
• [BioC] Removal of duplicate probes   James W. MacDonald
• [BioC] bioc data set not found   James W. MacDonald
• [BioC] affy code archeology: expresso behavior for liwong/invariantset   James W. MacDonald
• [BioC] Oligo - oligo::probeNames() returns transcript clusters, not probe sets   James W. MacDonald
• [BioC] Question about model design in limma   James W. MacDonald
• [BioC] LogFC query in Limma   James W. MacDonald
• [BioC] LogFC query in Limma   James W. MacDonald
• [BioC] how to supply a vector/list of results to GenTable in topGO?   Aaron Mackey
• [BioC] lowest common ancestor   Alyaa Mahmoud
• [BioC] getGEO error   Alyaa Mahmoud
• [BioC] getGEO error   Alyaa Mahmoud
• [BioC] getGEO error   Alyaa Mahmoud
• [BioC] phenoTest and variable-wise multiple testing   Jon Manning
• [BioC] phenoTest and variable-wise multiple testing   Jon Manning
• [BioC] EdgeR Time Series Design leading to unequal replicates   Marcelo
• [BioC] Using fRMA with "alternative" CDF files   Matthew McCall
• [BioC] Using fRMA with "alternative" CDF files   Matthew McCall
• [BioC] flowCore log transformation   Mike
• [BioC] flowCore log transformation   Mike
• [BioC] FlowCore - read.flowSet   Mike
• [BioC] FlowCore - read.flowSet   Mike
• [BioC] Adjusting microarray data using ComBat and SVA   Mirza, Nasir
• [BioC] DNA motif sequence prediction - finding a method to compare with   Faheem Mitha
• [BioC] Bioconductor Cloud AMI   Martin Morgan
• [BioC] normalise many cel files TCBB-2007-11-0161_noCEL.tar   Martin Morgan
• [BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow   Martin Morgan
• [BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow   Martin Morgan
• [BioC] BAM files to Genomic Ranges object   Martin Morgan
• [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname   Martin Morgan
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Martin Morgan
• [BioC] new package for generating interactive HTML reports   Martin Morgan
• [BioC] Course: Intermediate R / Bioconductor for High-Throughput Sequence Analysis, 14-15 Feb, Seattle   Martin Morgan
• [BioC] Using summarizeOverlaps with multiple samples/readgroups in a single bam file?   Martin Morgan
• [BioC] Turning a GRanges Metadata Column into Rle List   Martin Morgan
• [BioC] error installing KEGGSOAP   Martin Morgan
• [BioC] error installing KEGGSOAP   Martin Morgan
• [BioC] error installing KEGGSOAP   Martin Morgan
• [BioC] cummeRbund masks featureNames and samples from Biobase   Martin Morgan
• [BioC] cummeRbund masks featureNames and samples from Biobase   Martin Morgan
• [BioC] Transformation of Grange object to density per bin   Martin Morgan
• [BioC] [devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?   Martin Morgan
• [BioC] [devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?   Martin Morgan
• [BioC] R 2.15.2 trouble   Martin Morgan
• [BioC] Using summarizeOverlaps with multiple samples/readgroups in a single bam file?   Martin Morgan
• [BioC] shortread error?   Martin Morgan
• [BioC] split(SE, seqnames(SE)) doesn't work anymore   Martin Morgan
• [BioC] rhdf5 and factors   Martin Morgan
• [BioC] getAnnMap: package hgu95av2 not available   Martin Morgan
• [BioC] affy code archeology: expresso behavior for liwong/invariantset   Martin Morgan
• [BioC] Course reminder: Intermediate R / Bioc for Sequence Analysis   Martin Morgan
• [BioC] how to understand the concept metadata in bioconductor   Martin Morgan
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   Martin Morgan
• [BioC] GSEABase error parsing msigdb_v3.1.xml   Martin Morgan
• [BioC] rhdf5 and factors   Martin Morgan
• [BioC] Stay in touch with me through LinkedIn   Shreyartha Mukherjee
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Kamesh Narasimhan
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Kamesh Narasimhan
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Kamesh Narasimhan
• [BioC] Transformation of Grange object to density per bin   Hermann Norpois
• [BioC] Transformation of Grange object to density per bin   Hermann Norpois
• [BioC] Transformation of Grange object to density per bin   Hermann Norpois
• [BioC] Transformation of Grange object to density per bin   Hermann Norpois
• [BioC] Transformation of Grange object to density per bin   Hermann Norpois
• [BioC] Using GenomicRanges with table data   Tom Oates
• [BioC] Using GenomicRanges with table data   Tom Oates
• [BioC] ComBat   Valerie Obenchain
• [BioC] Empty Granges   Valerie Obenchain
• [BioC] ComBat   Valerie Obenchain
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Valerie Obenchain
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Valerie Obenchain
• [BioC] merging VCF files   Valerie Obenchain
• [BioC] seqlevels in VCF objects   Valerie Obenchain
• [BioC] VCF predictCoding(...) providing inconsistent results?   Valerie Obenchain
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Valerie Obenchain
• [BioC] VCF predictCoding(...) providing inconsistent results?   Valerie Obenchain
• [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs   Valerie Obenchain
• [BioC] Error when splitting an AAStringSet   Valerie Obenchain
• [BioC] unpackVcf not found   Valerie Obenchain
• [BioC] Getting Introns Expression at a Per Gene Level   Valerie Obenchain
• [BioC] VariantAnnotation: fine define Locating variants in and around genes   Valerie Obenchain
• [BioC] VariantAnnotation: fine define Locating variants in and around genes   Valerie Obenchain
• [BioC] get pixel coordinates interactively with EBimage   Andrzej Oleś
• [BioC] paper - download - pubmed   Nooshin Omranian
• [BioC] paper - download - pubmed   Nooshin Omranian
• [BioC] paper - download - pubmed   Nooshin Omranian
• [BioC] paper - download - pubmed   Nooshin Omranian
• [BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] countMatches() (was: table for GenomicRanges)   Hervé Pagès
• [BioC] Turning a GRanges Metadata Column into Rle List   Hervé Pagès
• [BioC] strategy to match/align peptide sequence to protein   Hervé Pagès
• [BioC] Bos taurus genome   Hervé Pagès
• [BioC] BAM files to Genomic Ranges object   Hervé Pagès
• [BioC] BAM files to Genomic Ranges object   Hervé Pagès
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Hervé Pagès
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Hervé Pagès
• [BioC] BAM files to Genomic Ranges object   Hervé Pagès
• [BioC] BAM files to Genomic Ranges object   Hervé Pagès
• [BioC] Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x   Hervé Pagès
• [BioC] Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x   Hervé Pagès
• [BioC] BSgenome forging - Node stack overflow   Hervé Pagès
• [BioC] Error - BSgenomeForge function   Hervé Pagès
• [BioC] Transformation of Grange object to density per bin   Hervé Pagès
• [BioC] BAM files to Genomic Ranges object   Hervé Pagès
• [BioC] Error when splitting an AAStringSet   Hervé Pagès
• [BioC] SNPlocs -> VCF or similar   Hervé Pagès
• [BioC] new package for generating interactive HTML reports   Xavier de Pedro
• [BioC] new package for generating interactive HTML reports   Xavier de Pedro
• [BioC] Oligo - oligo::probeNames() returns transcript clusters, not probe sets   James Perkins
• [BioC] shortread error?   Wang Peter
• [BioC] shortread error?   Wang Peter
• [BioC] how to understand the concept metadata in bioconductor   Wang Peter
• [BioC] how to understand the concept metadata in bioconductor   Wang Peter
• [BioC] how to understand the concept metadata in bioconductor   Wang Peter
• [BioC] how to understand the concept metadata in bioconductor   Wang Peter
• [BioC] how to understand the concept metadata in bioconductor   Wang Peter
• [BioC] status of visnab   Abhishek Pratap
• [BioC] status of visnab   Abhishek Pratap
• [BioC] help with visualizing structural variation data   Abhishek Pratap
• [BioC] help with visualizing structural variation data   Abhishek Pratap
• [BioC] help with visualizing structural variation data   Abhishek Pratap
• [BioC] getting an error with ggbio   Abhishek Pratap
• [BioC] getting an error with ggbio   Abhishek Pratap
• [BioC] quick question : creating ideogram for a in-house genome   Abhishek Pratap
• [BioC] ggbio : misplaced tracks in a test case   Abhishek Pratap
• [BioC] ggbio : misplaced tracks in a test case   Abhishek Pratap
• [BioC] setting contrast in edgeR   Alpesh Querer
• [BioC] Reading CEL files in using BufferedMatrix.justRMA   Emma Reick
• [BioC] is it possible to find sample batch # in CEL files?   James F. Reid
• [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?   René
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Alejandro Reyes
• [BioC] Efficiently running DEXSeq for Large Cohorts   Alejandro Reyes
• [BioC] Efficiently running DEXSeq for Large Cohorts   Alejandro Reyes
• [BioC] Efficiently running DEXSeq for Large Cohorts   Alejandro Reyes
• [BioC] Efficiently running DEXSeq for Large Cohorts   Alejandro Reyes
• [BioC] Efficiently running DEXSeq for Large Cohorts   Alejandro Reyes
• [BioC] DEXSeq package - read.HTSeqCount function error   Alejandro Reyes
• [BioC] DEXSeq and parallel, orphan processes.   Alejandro Reyes
• [BioC] DEXSeq: building exon count set   Alejandro Reyes
• [BioC] DEXSeq: building exon count set   Alejandro Reyes
• [BioC] Nimblegen arrays; random probes   Todd Richmond
• [BioC] affy annotation database   Paul Rigor
• [BioC] Nimblegen arrays; random probes   María José Rivas
• [BioC] Nimblegen arrays; random probes   María José Rivas
• [BioC] edgeR continuous variables   Mark Robinson
• [BioC] Advanced RNA-Seq and ChiP-Seq Data Analysis Course, 3-6 June 2013   Gabriella Rustici
• [BioC] DEXSeq estimating dispersions and multiple conditions   Natasha Sahgal
• [BioC] DEXSeq estimating dispersions and multiple conditions   Natasha Sahgal
• [BioC] DEXSeq estimating dispersions and multiple conditions   Natasha Sahgal
• [BioC] limma, voom, weights: factorial versus nested interaction results   Reiner Schulz
• [BioC] limma, voom, weights: factorial versus nested interaction results   Reiner Schulz
• [BioC] limma, voom, weights: factorial versus nested interaction results   Reiner Schulz
• [BioC] limma, voom, weights: factorial versus nested interaction results   Reiner Schulz
• [BioC] limma, voom, weights: factorial versus nested interaction results   Reiner Schulz
• [BioC] easyRNAseq remove overlapping features   Vincent Schulz
• [BioC] significance of correlation genes/miRNAs expression   Seb
• [BioC] using easyRNASeq to calculate RPKM values   Fatemehsadat Seyednasrollah
• [BioC] using easyRNASeq to calculate RPKM values   Fatemehsadat Seyednasrollah
• [BioC] Error message (probably) from AffyBatch.R when using a modified CDF   Hugh Shanahan
• [BioC] Error message (probably) from AffyBatch.R when using a modified CDF   Hugh Shanahan
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Paul Shannon
• [BioC] DNA motif sequence prediction - finding a method to compare with   Paul Shannon
• [BioC] geneid to gene name conversion   Paul Shannon
• [BioC] geneid to gene name conversion   Paul Shannon
• [BioC] cytoscapePlot() from graphite package   Paul Shannon
• [BioC] cytoscapePlot() from graphite package   Paul Shannon
• [BioC] KEGGgraph problem   Paul Shannon
• [BioC] Filtering out duplicate probes in Affy data   Himanshu Sharma
• [BioC] Filtering out duplicate probes in Affy data   Himanshu Sharma
• [BioC] differential expression analysis for 1 vs 1 experiment   Himanshu Sharma
• [BioC] Removal of duplicate probes   Himanshu Sharma
• [BioC] normalization of illumina bead array data   Wei Shi
• [BioC] Limma Voom R package   Wei Shi
• [BioC] normalization of illumina bead array data   Wei Shi
• [BioC] normalization of illumina bead array data   Wei Shi
• [BioC] biomaRt query: retrieve exon locations etc   Tim Smith
• [BioC] limma, voom, weights: factorial versus nested interaction results   Gordon K Smyth
• [BioC] limma, voom, weights: factorial versus nested interaction results   Gordon K Smyth
• [BioC] Double KO and timecourse design / limma   Gordon K Smyth
• [BioC] Double KO and timecourse design / limma   Gordon K Smyth
• [BioC] detailed analysis process of Comparisons Both Between and Within Subjects of edgeR   Gordon K Smyth
• [BioC] limma design and contrast matrix for paired experiment   Gordon K Smyth
• [BioC] Limma and XML   Gordon K Smyth
• [BioC] limma design and contrast matrix for paired experiment   Gordon K Smyth
• [BioC] limma design and contrast matrix for paired experiment   Gordon K Smyth
• [BioC] edgeR logFC   Gordon K Smyth
• [BioC] normalization of illumina bead array data   Gordon K Smyth
• [BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp   Gordon K Smyth
• [BioC] Query regarding limma   Gordon K Smyth
• [BioC] DiffBind error   Rory Stark
• [BioC] DiffBind error   Rory Stark
• [BioC] Turning a GRanges Metadata Column into Rle List   Aaron Statham
• [BioC] Turning a GRanges Metadata Column into Rle List   Aaron Statham
• [BioC] BiomaRt: getLDS keeps returning NULL   Steven
• [BioC] BiomaRt: getLDS keeps returning NULL   Steven
• [BioC] Turning a GRanges Metadata Column into Rle List   Dario Strbenac
• [BioC] Turning a GRanges Metadata Column into Rle List   Dario Strbenac
• [BioC] BAM files to Genomic Ranges object   Dario Strbenac
• [BioC] BAM files to Genomic Ranges object   Dario Strbenac
• [BioC] Turning a GRanges Metadata Column into Rle List   Dario Strbenac
• [BioC] BAM files to Genomic Ranges object   Dario Strbenac
• [BioC] Transformation of Grange object to density per bin   Dario Strbenac
• [BioC] paper - download - pubmed   Chris Stubben
• [BioC] paper - download - pubmed   Chris Stubben
• [BioC] paper - download - pubmed   Chris Stubben
• [BioC] Query regarding limma   Roopa Subbaiaih
• [BioC] Query regarding limma   Roopa Subbaiaih
• [BioC] LogFC query in Limma   Roopa Subbaiaih
• [BioC] LogFC query in Limma   Roopa Subbaiaih
• [BioC] LogFC query in Limma   Roopa Subbaiaih
• [BioC] 答复: edgeR version   Guiling Sun
• [BioC] [devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?   Renjie Tan
• [BioC] GEOquery getGEO error in read.table   Dave Tang
• [BioC] GEOquery getGEO error in read.table   Dave Tang
• [BioC] Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA   Tarca, Adi
• [BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow   Murat Tasan
• [BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow   Murat Tasan
• [BioC] seqlevels in VCF objects   Murat Tasan
• [BioC] seqlevels in VCF objects   Murat Tasan
• [BioC] VCF predictCoding(...) providing inconsistent results?   Murat Tasan
• [BioC] VCF predictCoding(...) providing inconsistent results?   Murat Tasan
• [BioC] Open PhD and PostDoc Position in Bioinformatics at Goethe University, Frankfurt, Germany   Stefanie Tauber
• [BioC] Error in Installing BioBase Development version   Dan Tenenbaum
• [BioC] RankAggreg package   Dan Tenenbaum
• [BioC] error message relating to png file when running maQualityPlots   Dan Tenenbaum
• [BioC] error message relating to png file when running maQualityPlots   Dan Tenenbaum
• [BioC] status of visnab   Dan Tenenbaum
• [BioC] IMA Peak Correction Error - subscript out of bounds   Dan Tenenbaum
• [BioC] Problem in KEGGSOAP package   Dan Tenenbaum
• [BioC] GEOquery getGEO error in read.table   Dan Tenenbaum
• [BioC] Error installing iFlow   Dan Tenenbaum
• [BioC] DESeq package error   Dan Tenenbaum
• [BioC] topGO quick start guide error   Dan Tenenbaum
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Dan Tenenbaum
• [BioC] KEGGREST package is available in devel   Dan Tenenbaum
• [BioC] error installing KEGGSOAP   Dan Tenenbaum
• [BioC] error installing KEGGSOAP   Dan Tenenbaum
• [BioC] annmap installation window   Dan Tenenbaum
• [BioC] error installing KEGGSOAP   Dan Tenenbaum
• [BioC] error installing KEGGSOAP   Dan Tenenbaum
• [BioC] error installing KEGGSOAP   Dan Tenenbaum
• [BioC] KEGG REST: retrieving genes   Dan Tenenbaum
• [BioC] detailed analysis process of "Comparisons Both Between and Within Subjects" of edgeR   Huajing Teng
• [BioC] detailed analysis process of \"Comparisons Both Between   Huajing Teng
• [BioC] Using different file formats with oligo and analysis packages using oligo   Hans Thompson
• [BioC] limma, voom, weights: factorial versus nested interaction results   Ryan C. Thompson
• [BioC] setting contrast in edgeR   Ryan C. Thompson
• [BioC] detailed analysis process of \"Comparisons Both Between and Within Subjects\" of edgeR   Ryan C. Thompson
• [BioC] detailed analysis process of \"Comparisons Both Between and Within Subjects\" of edgeR   Ryan C. Thompson
• [BioC] detailed analysis process of \"Comparisons Both Between   Ryan C. Thompson
• [BioC] limma, voom, weights: factorial versus nested interaction results   Ryan C. Thompson
• [BioC] Using summarizeOverlaps with multiple samples/readgroups in a single bam file?   Ryan C. Thompson
• [BioC] edgeR logFC   Ryan C. Thompson
• [BioC] Using summarizeOverlaps with multiple samples/readgroups in a single bam file?   Ryan C. Thompson
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] status of visnab   Tim Triche, Jr.
• [BioC] status of visnab   Tim Triche, Jr.
• [BioC] Turning a GRanges Metadata Column into Rle List   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] countMatches() (was: table for GenomicRanges)   Tim Triche, Jr.
• [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname   Tim Triche, Jr.
• [BioC] Pasilla data for "Counting with summarizeOverlaps/GenomicRanges"   Tim Triche, Jr.
• [BioC] Using GenomicRanges with table data   Tim Triche, Jr.
• [BioC] Transformation of Grange object to density per bin   Tim Triche, Jr.
• [BioC] split(SE, seqnames(SE)) doesn't work anymore   Tim Triche, Jr.
• [BioC] split(SE, seqnames(SE)) doesn't work anymore   Tim Triche, Jr.
• [BioC] split(SE, seqnames(SE)) doesn't work anymore   Tim Triche, Jr.
• [BioC] Best Package To Normalize Microarray Data with Few Samples   Tim Triche, Jr.
• [BioC] how to understand the concept metadata in bioconductor   Tim Triche, Jr.
• [BioC] how to understand the concept metadata in bioconductor   Tim Triche, Jr.
• [BioC] how to understand the concept metadata in bioconductor   Tim Triche, Jr.
• [BioC] how to understand the concept metadata in bioconductor   Tim Triche, Jr.
• [BioC] VariantAnnotation: fine define Locating variants in and around genes   Fabrice Tourre
• [BioC] VariantAnnotation: fine define Locating variants in and around genes   Fabrice Tourre
• [BioC] is it possible to find sample batch # in CEL files?   Brian Tsai
• [BioC] ASN.1   Ben Tupper
• [BioC] ASN.1   Ben Tupper
• [BioC] We've posted our 2013***R Courses*** by XLSolutions Corp at 9 USA Cities: San Francisco, New York, Washington DC, Houston, Boston, Las Vegas, Seattle, etc   Sue Turner
• [BioC] Problems with 'affxparser' package   Valor Becerra, Luis Miguel
• [BioC] Problems with 'affxparser' package   Valor Becerra, Luis Miguel
• [BioC] Problems with 'affxparser' package   Valor Becerra, Luis Miguel
• [BioC] DEXSeq: problem with dexseq_prepare_annotation.py   Geetha Venkatesh
• [BioC] [OT] Job Opening: Bioinformatician at OpenAnalytics (Belgium)   Tobias Verbeke
• [BioC] Best Package To Normalize Microarray Data with Few Samples   Gundala Viswanath
• [BioC] Variability Plot For Toray Microarray Data   Gundala Viswanath
• [BioC] Meaning of Median and IQR in MA-Plot, Affy Package   Gundala Viswanath
• [BioC] marray maQualityPlots error   Pavlík Vojtěch
• [BioC] limma design and contrast matrix for paired experiment   David Westergaard
• [BioC] limma design and contrast matrix for paired experiment   David Westergaard
• [BioC] annmap installation window   Tim Yates
• [BioC] Class for a DataFrame of Matrices   Tim Yates
• [BioC] Class for a DataFrame of Matrices   Tim Yates
• [BioC] DEXSeq and parallel, orphan processes.   Bin Ye
• [BioC] DEXSeq and parallel, orphan processes.   Bin Ye
• [BioC] status of visnab   Tengfei Yin
• [BioC] help with visualizing structural variation data   Tengfei Yin
• [BioC] ggsave option for ggbio Tracks function   Tengfei Yin
• [BioC] ggsave option for ggbio Tracks function   Tengfei Yin
• [BioC] ggbio : misplaced tracks in a test case   Tengfei Yin
• [BioC] ggbio : misplaced tracks in a test case   Tengfei Yin
• [BioC] rtracklayer export method requires unique names   Samuel Younkin
• [BioC] snpStats --- MAF in Pedigrees   Samuel Younkin
• [BioC] KEGGgraph problem   Zhang, Jitao David
• [BioC] DESeq - working with more than 2 conditions   Shanrong Zhao
• [BioC] ChIPpeakAnno/IRanges - getAllPeakSequence(data, upstream = 25, downstream = 25, genome=Mmusculus)   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno/IRanges - getAllPeakSequence(data, upstream = 25, downstream = 25, genome=Mmusculus)   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno/IRanges - getAllPeakSequence(data, upstream = 25, downstream = 25, genome=Mmusculus)   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno/IRanges - getAllPeakSequence(data, upstream = 25, downstream = 25, genome=Mmusculus)   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   Zhu, Lihua (Julie)
• [BioC] Error installing iFlow   Jacques Fattaccioli [ENS]
• [BioC] Coercing Agilent two colour microarray data into CHARM   Andrew Beggs [guest]
• [BioC] annmap installation window   Chris Banerji [guest]
• [BioC] Agilent Chip G4858A-039494: columns gTotalGeneSignal, gTotalProbeSignal missing for AgiMicroRna   Constanze [guest]
• [BioC] affy code archeology: expresso behavior for liwong/invariantset   David Eby [guest]
• [BioC] Problem with biomaRt update in R-2.15.1   Eleni Christodoulou [guest]
• [BioC] Plotting Broad HMM states in Gviz   Elmar Tobi [guest]
• [BioC] cummeRbund masks featureNames and samples from Biobase   Francois Lefebvre [guest]
• [BioC] annotations   Gonzalo Brugues [guest]
• [BioC] edgeR version   Guiling Sun [guest]
• [BioC] ComBat:covariates or additional batch   Hedi Peterson [guest]
• [BioC] detailed analysis process of \"Comparisons Both Between and Within Subjects\" of edgeR   Huajing Teng [guest]
• [BioC] Problems in running easyRNASeq   Jeya [guest]
• [BioC] Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands   Joseph Siefert [guest]
• [BioC] Difficulties in using the mgsa package for Gene Set Analysis   Juan M.Adrian [guest]
• [BioC] R 2.15.2 trouble   Julie Tseng-Crank [guest]
• [BioC] Normalization   Leandro [guest]
• [BioC] Can we use DNAcopy to analyse Copy Number Viaration using next generation sequencing data generated by eigher Ion PGM or Illumina MiSeq   Min Wang [guest]
• [BioC] Loading Data into MethyAnalysis   Ranya [guest]
• [BioC] IMA Peak Correction Error - subscript out of bounds   Scott Robinson [guest]
• [BioC] GO graphs made with topGO are unreadable   Sini [guest]
• [BioC] RankAggreg package   Taraka Ramji M [guest]
• [BioC] Gene Ontology: Shortest path from root to node   WoA [guest]
• [BioC] GLM in DEseq   Yahb [guest]
• [BioC] error message relating to png file when running maQualityPlots   Yanqing Hu [guest]
• [BioC] getAnnMap: package hgu95av2 not available   elva chen [guest]
• [BioC] KEGGgraph problem   eric [guest]
• [BioC] R error by installing the org.Hs.eg.db package   lisann [guest]
• [BioC] AgiMicroRna problem   maryam shahmansoori [guest]
• [BioC] reading data in AgiMicroRna package   maryam shahmansouri [guest]
• [BioC] normalise many cel files TCBB-2007-11-0161_noCEL.tar   wlangdon [guest]
• [BioC] normalization of illumina bead array data   michele caseposta
• [BioC] normalization of illumina bead array data   michele caseposta
• [BioC] normalization of illumina bead array data   michele caseposta
• [BioC] normalization of illumina bead array data   michele caseposta
• [BioC] normalization of illumina bead array data   michele caseposta
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] error installing KEGGSOAP   array chip
• [BioC] cytoscapePlot() from graphite package   array chip
• [BioC] cytoscapePlot() from graphite package   array chip
• [BioC] cytoscapePlot() from graphite package   array chip
• [BioC] edgeR logFC   chris_utah
• [BioC] edgeR logFC   chris_utah
• [BioC] biomaRt error   chris_utah
• [BioC] is it possible to find sample batch # in CEL files?   Rob.Dunne at csiro.au
• [BioC] Question about model design in limma   Tim.Peters at csiro.au
• [BioC] xps: hugene11 chip gives problems   cstrato
• [BioC] xps: hugene11 chip gives problems   cstrato
• [BioC] xps: hugene11 chip gives problems   cstrato
• [BioC] xps installation question   cstrato
• [BioC] about ComBat plot for non parametric   hu duan
• [BioC] RNA Seq Profiling Experiment   empyrean999
• [BioC] ‘AnnotationForge’ is not available for Linux system??   capricy gao
• [BioC] ‘AnnotationForge’ is not available for Linux system??   capricy gao
• [BioC] World’s Biggest Computer Conference WORLDCOMP is Cancelled   amgsolo at hushmail.com
• [BioC] WORLDCOMP: World’s Biggest Bogus Conference is Back Again   kelvinwilliams at hushmail.com
• [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS   kamesh
• [BioC] normalise many cel files TCBB-2007-11-0161_noCEL.tar   w langdon
• [BioC] Bioconductor Digest, Vol 119, Issue 1   w langdon
• [BioC] unpackVcf not found   seth redmond
• [BioC] error installing KEGGSOAP   zhao shilin
• [BioC] need help regarding quality assessment of raw data   varshika singh
• [BioC] Overrepresentation pathway with KEGGPROFILE and SPIA   slzhao
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] BAM files to Genomic Ranges object   jluis.lavin at unavarra.es
• [BioC] DiffBind error   jluis.lavin at unavarra.es
• [BioC] DiffBind error   jluis.lavin at unavarra.es
• [BioC] DiffBind error   jluis.lavin at unavarra.es
• [BioC] AUTO: Pie Müller is out of the office. (returning 31.01.2013)   Pie.Mueller at unibas.ch
• [BioC] Overrepresentation pathway with KEGGPROFILE and SPIA   gregory voisin
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   hickey at wehi.EDU.AU
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   hickey at wehi.EDU.AU
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   hickey at wehi.EDU.AU
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   hickey at wehi.EDU.AU
• [BioC] Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges   hickey at wehi.EDU.AU
• [BioC] bioc data set not found   carol white

Last message date: Thu Jan 31 23:24:07 CET 2013
Archived on: Thu Jan 31 23:24:56 CET 2013

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