December 2013 Archives by author

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Starting: Sun Dec 1 03:21:00 CET 2013
Ending: Tue Dec 31 22:47:47 CET 2013
Messages: 472

• [BioC] Plink Data for Fst Calculations   Ovokeraye Achinike-Oduaran
• [BioC] edgeR on ncRNA analysis question   Genomnia - Guffanti Alessandro
• [BioC] edgeR on ncRNA analysis question   Genomnia - Guffanti Alessandro
• [BioC] XCMS for LC-MS   Bashar Amer
• [BioC] XCMS for LC-MS   Bashar Amer
• [BioC] Can DESeq2 find tissue-specific expression genes   Simon Anders
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Simon Anders
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Simon Anders
• [BioC] DEXseq: fitDispersionFunction error   Simon Anders
• [BioC] Calculate BCV in edgeR - sample without replicates   Atul
• [BioC] Limma for DNA methylation arrays?   Gustavo Fernandez Bayon
• [BioC] Questions on Combat in methylation data Thank you for your help   Gustavo Fernández Bayón
• [BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable errorR   Eugene Bolotin
• [BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable errorR   Eugene Bolotin
• [BioC] rhdf5 segfault   Ben Bolstad
• [BioC] HGNC annotation for use in GOstats   Boel Brynedal
• [BioC] HGNC annotation for use in GOstats   Boel Brynedal
• [BioC] Using gene symbols as labels for heatmap instead of microarray ID   António Brito Camacho
• [BioC] Using gene symbols as labels for heatmap instead of microarray ID   António Brito Camacho
• [BioC] Using gene symbols as labels for heatmap instead of microarray ID   António Brito Camacho
• [BioC] remove evidence Codes   Vincent Carey
• [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?   Marc Carlson
• [BioC] subset a RleList using GRanges object?   Robert Castelo
• [BioC] subset a RleList using GRanges object?   Robert Castelo
• [BioC] Bug in subsetting vcf file by subject on more than 5 samples   Robert Castelo
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Robert Castelo
• [BioC] bug in graph::addNode() w/ graph::edgeData()   Robert Castelo
• [BioC] Fitting linear model with different design matrix for each gene in limma   Can Cenik
• [BioC] Question about MEDIPS extend parameter   Lukas Chavez
• [BioC] using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Lukas Chavez
• [BioC] RNA-Seq fold change compared to control, without replicates   Lisa Cohen
• [BioC] subset a RleList using GRanges object?   Cook, Malcolm
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Cook, Malcolm
• [BioC] subset a RleList using GRanges object?   Cook, Malcolm
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Cook, Malcolm
• [BioC] subset a RleList using GRanges object?   Cook, Malcolm
• [BioC] error in "count" for SummarizedExperiment in easyRNASeq   Malcolm Cook
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Kevin Coombes
• [BioC] Gene shaving for bioconductor?   Kevin Coombes
• [BioC] edgeR glmFit   Jahn Davik
• [BioC] Case vs Control Information,Diseases   Sean Davis
• [BioC] Meta data for gene from GEO   Sean Davis
• [BioC] Install older version of Bioconductor   Sean Davis
• [BioC] Analysing Affy data with limma   Sean Davis
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Davis, Wade
• [BioC] easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information   Nicolas Delhomme
• [BioC] easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information   Nicolas Delhomme
• [BioC] DB PROBLEM   Nicolas Delhomme
• [BioC] Oryza sativa problem   Nicolas Delhomme
• [BioC] alphabetByCycle not working on AAStringSet   Nicolas Delhomme
• [BioC] error in "count" for SummarizedExperiment in easyRNASeq   Nicolas Delhomme
• [BioC] GLAD crashes when built with gcc-4.8   Ramon Diaz-Uriarte
• [BioC] GLAD crashes when built with gcc-4.8   Ramon Diaz-Uriarte
• [BioC] Issue installing rhdf5 package on R-3.0.2   Bernd Fischer
• [BioC] Issue installing rhdf5 package on R-3.0.2   Bernd Fischer
• [BioC] BiocStyle short header   Bernd Fischer
• [BioC] GWASTools suggestions: explicit interface for GenotypeReaders,   Karl Forner
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Gilgi Friedlander
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Gilgi Friedlander
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Gilgi Friedlander
• [BioC] rhdf5 segfault   Brad Friedman
• [BioC] rhdf5 segfault   Brad Friedman
• [BioC] (adj.p.value & log2FC) or (B.value & log2FC)   Richard Friedman
• [BioC] simultaneous use of robust and weighting methods in limma.   Richard Friedman
• [BioC] Error message using arrayweights   Richard Friedman
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Paul Geeleher
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Julian Gehring
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Julian Gehring
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Julian Gehring
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Julian Gehring
• [BioC] Package SomaticCancerAlterations, import own .maf file?   Julian Gehring
• [BioC] Package SomaticCancerAlterations, import own .maf file?   Julian Gehring
• [BioC] kmer and zscore calculation   Julian Gehring
• [BioC] kmer and zscore calculation   Julian Gehring
• [BioC] ggbio: mirrored coverage plots for +/- strands   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Thomas Girke
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Christine Gläßer
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Christine Gläßer
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Christine Gläßer
• [BioC] GWASTools suggestions: explicit interface for GenotypeReaders,   Stephanie M. Gogarten
• [BioC] Job opening: Research Scientist in Biostatistics (Seattle, WA)   Stephanie M. Gogarten
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   María Maqueda González
• [BioC] RCytoscape: object 'graph' not found error   Christopher T Gregg
• [BioC] RCytoscape: object 'graph' not found error   Christopher T Gregg
• [BioC] RCytoscape: object 'graph' not found error   Christopher T Gregg
• [BioC] XCMS for LC-MS   Ivan Gregoretti
• [BioC] [ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids   Jason Hackney
• [BioC] Gviz - Visualize Reads - Color by Presence of Junction?   Hahne, Florian
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Hahne, Florian
• [BioC] RmiR and RmiR.Hs.miRNA   Thomas H. Hampton
• [BioC] Illumina Expression analysis from iDAT files   Kasper Daniel Hansen
• [BioC] minfi release 1.8   Kasper Daniel Hansen
• [BioC] How do I remove bad samples/probes before normalization and SWAN?   Kasper Daniel Hansen
• [BioC] Reading IDAT files with illuminaio   Kasper Daniel Hansen
• [BioC] Rgraphviz installation issue   Kasper Daniel Hansen
• [BioC] XCMS for LC-MS   Kasper Daniel Hansen
• [BioC] Rgraphviz installation issue   Kasper Daniel Hansen
• [BioC] Rgraphviz installation issue   Kasper Daniel Hansen
• [BioC] Converting single GRanges object as per chromosome GRangeList   Prashantha Hebbar
• [BioC] Converting single GRanges object as per chromosome GRangeList   Prashantha Hebbar
• [BioC] matchPattern vmatchPattern vectorised   Henderson, Stephen
• [BioC] matchPattern vmatchPattern vectorised   Henderson, Stephen
• [BioC] matchPattern vmatchPattern vectorised   Henderson, Stephen
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Aliaksei Holik
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Aliaksei Holik
• [BioC] SmearPlot edgeR - adding gene names to genes of interest   Aliaksei Holik
• [BioC] Using gene symbols as labels for heatmap instead of microarray ID   Aliaksei Holik
• [BioC] a question about getGEO function   Nazanin Hosseinkhan
• [BioC] Separating gene filtering and multiple testing p-value adjustment steps   Wolfgang Huber
• [BioC] affyPLM crashing R   Wolfgang Huber
• [BioC] hoeffd function (CRAN HMisc package) use in arrayQualityMetrics   Wolfgang Huber
• [BioC] arrayQualityMetrics does not produce interactive plots   Wolfgang Huber
• [BioC] rhdf5 segfault   Wolfgang Huber
• [BioC] rhdf5 segfault   Wolfgang Huber
• [BioC] Gviz - Visualize Reads - Color by Presence of Junction?   Robert Ivanek
• [BioC] Gviz - Visualize Reads - Color by Presence of Junction?   Andrew Jaffe
• [BioC] rhdf5 segfault   Harris A. Jaffee
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Jailwala, Parthav (NIH/NCI) [C]
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Jailwala, Parthav (NIH/NCI) [C]
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Jailwala, Parthav (NIH/NCI) [C]
• [BioC] which genes to choose for being truly differentially expressed from a long list   Ekta Jain
• [BioC] which genes to choose for being truly differentially expressed from a long list   Ekta Jain
• [BioC] Apply non-Gaussian distribution data to limma   JiangZhengyu
• [BioC] Questions on Combat in methylation data Thank you for your help   Johnson, William Evan
• [BioC] Scaling sRNA/degradome libraries - edgeR   Atul Kakrana
• [BioC] Calculate BCV in edgeR - sample without replicates   Atul Kakrana
• [BioC] Calculate BCV in edgeR - sample without replicates   Atul Kakrana
• [BioC] DiffBind Error.   Kasthuri Kannan
• [BioC] DiffBind Error.   Kannan, Kasthuri
• [BioC] DiffBind Error.   Kannan, Kasthuri
• [BioC] DiffBind Error.   Kannan, Kasthuri
• [BioC] topGO spurious GO terms?   Jan Kim
• [BioC] DESeq problem   Günter Klambauer
• [BioC] Limma makeContrasts - incorporating known confounder   Bernd Klaus
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   Federico Lasa
• [BioC] Bioconductor Digest, Vol 128, Issue 7   Federico Lasa
• [BioC] processing BamFiles - streaming vs not streaming   Michael Lawrence
• [BioC] subset a RleList using GRanges object?   Michael Lawrence
• [BioC] subset a RleList using GRanges object?   Michael Lawrence
• [BioC] subset a RleList using GRanges object?   Michael Lawrence
• [BioC] subset a RleList using GRanges object?   Michael Lawrence
• [BioC] subset a RleList using GRanges object?   Michael Lawrence
• [BioC] ggbio: mirrored coverage plots for +/- strands   Michael Lawrence
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Michael Lawrence
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Michael Lawrence
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Michael Lawrence
• [BioC] RleList   Michael Lawrence
• [BioC] arrayQualityMetrics for Agilent one color data   Yong Li
• [BioC] edgeR   Steve Lianoglou
• [BioC] failed to install biocondoctuor   Steve Lianoglou
• [BioC] Converting single GRanges object as per chromosome GRangeList   Steve Lianoglou
• [BioC] prefiltering genelist before LIMMA & cut-off paramter for getting DEGs from topT object.   Steve Lianoglou
• [BioC] Dealing with probes with high fold change but PA call 0   Steve Lianoglou
• [BioC] Dealing with probes with high fold change but PA call 0   Steve Lianoglou
• [BioC] matchPattern vmatchPattern vectorised   Steve Lianoglou
• [BioC] kind request   Steve Lianoglou
• [BioC] time series data edgeR?   Steve Lianoglou
• [BioC] RNA-Seq fold change compared to control, without replicates   Steve Lianoglou
• [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?   Steve Lianoglou
• [BioC] Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field   Matthias Lienhard
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Matthias Lienhard
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Matthias Lienhard
• [BioC] Using a countDataSet as input data in DESeq2   Michael Love
• [BioC] cooksCutoff error   Michael Love
• [BioC] DESeq2(analysis without replicate)   Michael Love
• [BioC] DESeq(normalize using all samples?)   Michael Love
• [BioC] Multiple contrasts in DESeq2   Michael Love
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Michael Love
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Michael Love
• [BioC] mulitfactorial analysis, adjusting for quantitative covariates   James W. MacDonald
• [BioC] which genes to choose for being truly differentially expressed from a long list   James W. MacDonald
• [BioC] arrayQualityMetrics for Agilent one color data   James W. MacDonald
• [BioC] which genes to choose for being truly differentially expressed from a long list   James W. MacDonald
• [BioC] Why daisy() in cluster library failed to exclude NA when computing dissimilarity   James W. MacDonald
• [BioC] Apply non-Gaussian distribution data to limma   James W. MacDonald
• [BioC] HGNC annotation for use in GOstats   James W. MacDonald
• [BioC] Analysing Affy data with limma   James W. MacDonald
• [BioC] Testing main effects and interactions in edgeR without contrasts   James W. MacDonald
• [BioC] edgeR   James W. MacDonald
• [BioC] install geneplotter   James W. MacDonald
• [BioC] XCMS for LC-MS   James W. MacDonald
• [BioC] Fwd: Annotation discrepancy   James W. MacDonald
• [BioC] Fwd: Annotation discrepancy   James W. MacDonald
• [BioC] edgeR Design Matrix   James W. MacDonald
• [BioC] limma2annaffy   James W. MacDonald
• [BioC] edgeR Design Matrix   James W. MacDonald
• [BioC] FDR and Estimated Fragment length   James W. MacDonald
• [BioC] edgeR Design Matrix   James W. MacDonald
• [BioC] edgeR Design Matrix   James W. MacDonald
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Aaron Mackey
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Aaron Mackey
• [BioC] Useful information about Ensembl release 74 mart databases   Thomas Maurel
• [BioC] Problems Counting Reads with summarizeOverlaps   Sam McInturf
• [BioC] edgeR question   Sam McInturf
• [BioC] genomicRanges/Features reads counted in features and inbetween features is not the total number of counted reads   Sam McInturf
• [BioC] Problems Counting Reads with summarizeOverlaps   Sam McInturf
• [BioC] Problems Counting Reads with summarizeOverlaps   Sam McInturf
• [BioC] edgeR complex partial multifactorial design   Sam McInturf
• [BioC] edgeR prior.count   Karen Menuz
• [BioC] inconsistency in illuminaHumanv4.db?   P.D. Moerland
• [BioC] New Seattle Bioconductor group members   Martin Morgan
• [BioC] alphabetByCycle not working on AAStringSet   Martin Morgan
• [BioC] Best way to capture both NCBI and UCSC labeled alignments?   Martin Morgan
• [BioC] Using gene symbols as labels for heatmap instead of microarray ID   Martin Morgan
• [BioC] GLAD crashes when built with gcc-4.8   Martin Morgan
• [BioC] Limma makeContrasts - incorporating known confounder   Ed Mountjoy
• [BioC] package ā pasillaā is not available (for R version 3.0.2)   Jeremy Ng
• [BioC] Is ComBat introducing a signal where there is none?   Vegard Nygaard
• [BioC] Using Biostring to make position frequency matrix   Valerie Obenchain
• [BioC] Problems Counting Reads with summarizeOverlaps   Valerie Obenchain
• [BioC] Problems Counting Reads with summarizeOverlaps   Valerie Obenchain
• [BioC] Problems Counting Reads with summarizeOverlaps   Valerie Obenchain
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Valerie Obenchain
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Valerie Obenchain
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Valerie Obenchain
• [BioC] Bug in subsetting vcf file by subject on more than 5 samples   Valerie Obenchain
• [BioC] Problems Counting Reads with summarizeOverlaps   Valerie Obenchain
• [BioC] Problems Counting Reads with summarizeOverlaps   Valerie Obenchain
• [BioC] ensemblVEP, variant_effect_predictor versions and release schedule   Valerie Obenchain
• [BioC] MotifStack not plotting?   Ou, Jianhong
• [BioC] BSgenome.Mmulatta.UCSC   Hervé Pagès
• [BioC] subset a RleList using GRanges object?   Hervé Pagès
• [BioC] subset a RleList using GRanges object?   Hervé Pagès
• [BioC] subset a RleList using GRanges object?   Hervé Pagès
• [BioC] subset a RleList using GRanges object?   Hervé Pagès
• [BioC] BioStrings for current R: RE: BSgenomeForge seed file - seqnames field   Hervé Pagès
• [BioC] Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field   Hervé Pagès
• [BioC] subset a RleList using GRanges object?   Hervé Pagès
• [BioC] matchPattern vmatchPattern vectorised   Hervé Pagès
• [BioC] Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field   Hervé Pagès
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Hervé Pagès
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Hervé Pagès
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Hervé Pagès
• [BioC] kmer and zscore calculation   Hervé Pagès
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Hervé Pagès
• [BioC] Pairwise Alignment on Large Protein Sequence Data Set   Hervé Pagès
• [BioC] forgeSeqFiles   Hervé Pagès
• [BioC] substr on XStringSet-class   Hervé Pagès
• [BioC] BiomaRt & retrieving flanking regions   Hervé Pagès
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Lorena Pantano
• [BioC] problem with locateVariants   Mattia Pelizzola
• [BioC] Job: Postdoc positions - Computational Biology - Center for Genomic Science, Milan, Italy   Mattia Pelizzola
• [BioC] failed to install biocondoctuor   Wang Peter
• [BioC] failed to install biocondoctuor   Wang Peter
• [BioC] RleList   Massimo Petretich
• [BioC] kind request   Aneta Pluta
• [BioC] annotation package for HuEx-1_0-st-v1 platform instead of pd.huex.1.0.st.v1   Rahmatallah, Yasir
• [BioC] Error message using arrayweights   Matt Ritchie
• [BioC] edgeR DGEList   Mark Robinson
• [BioC] edgeR DGEList   Mark Robinson
• [BioC] edgeR glmFit   Mark Robinson
• [BioC] calcNormFactors gives NaN normalization values- Please Help!   Mark Robinson
• [BioC] edgeR glmFit   Mark Robinson
• [BioC] edgeR glmFit   Mark Robinson
• [BioC] differential expression- edgeR   Mark Robinson
• [BioC] differential expression- edgeR   Mark Robinson
• [BioC] affyPLM crashing R   Scott Robinson
• [BioC] affyPLM crashing R   Scott Robinson
• [BioC] affyPLM crashing R   Scott Robinson
• [BioC] a question about getGEO function   Simona Rossi
• [BioC] time series data edgeR?   Ryan
• [BioC] Calculate BCV in edgeR - sample without replicates   Ryan
• [BioC] Fitting linear model with different design matrix for each gene in limma   Ryan
• [BioC] calcNormFactors gives me NaN   Ryan
• [BioC] Fitting linear model with different design matrix for each gene in limma   Ryan
• [BioC] Calculate BCV in edgeR - sample without replicates   Ryan
• [BioC] DEXseq: fitDispersionFunction error   Uma Shankavaram
• [BioC] bug in graph::addNode() w/ graph::edgeData()   Paul Shannon
• [BioC] RCytoscape: object 'graph' not found error   Paul Shannon
• [BioC] RCytoscape: object 'graph' not found error   Paul Shannon
• [BioC] FYI: Junior bioinformatian positions available   Steve Shen
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Wei Shi
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Wei Shi
• [BioC] Testing main effects and interactions in edgeR without contrasts   David Shuker
• [BioC] Bioconductor Digest, Vol 128, Issue 7   Manvendra Singh
• [BioC] Problems Counting Reads with summarizeOverlaps   Reema Singh
• [BioC] Problems Counting Reads with summarizeOverlaps   Reema Singh
• [BioC] edgeR Design Matrix   Reema Singh
• [BioC] edgeR Design Matrix   Reema Singh
• [BioC] edge R exactTest output looks odd - PLEASE HELP!   Reema Singh
• [BioC] edgeR Design Matrix   Reema Singh
• [BioC] edgeR Design Matrix   Reema Singh
• [BioC] edgeR Design Matrix   Reema Singh
• [BioC] EdgeR glm based analysis   Reema Singh
• [BioC] BiomaRt & retrieving flanking regions   Greg Slodkowicz
• [BioC] BiomaRt & retrieving flanking regions   Greg Slodkowicz
• [BioC] BiomaRt & retrieving flanking regions   Greg Slodkowicz
• [BioC] Reading IDAT files with illuminaio   Mike Smith
• [BioC] edgeR on ncRNA analysis question   Gordon K Smyth
• [BioC] edgeR on ncRNA analysis question   Gordon K Smyth
• [BioC] limma - genas: unexpected warnings   Gordon K Smyth
• [BioC] easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information   Gordon K Smyth
• [BioC] (adj.p.value & log2FC) or (B.value & log2FC)   Gordon K Smyth
• [BioC] edgeR prior.count   Gordon K Smyth
• [BioC] edgeR   Gordon K Smyth
• [BioC] simultaneous use of robust and weighting methods in limma   Gordon K Smyth
• [BioC] Why the resuts are so different between the classic and the glm methods?   Gordon K Smyth
• [BioC] Testing main effects and interactions in edgeR without contrasts   Gordon K Smyth
• [BioC] Why the resuts are so different between the classic and the glm methods?   Gordon K Smyth
• [BioC] edgeR question (reading tab delimited files)   Gordon K Smyth
• [BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable errorR   Gordon K Smyth
• [BioC] DiffBind Error.   Rory Stark
• [BioC] DiffBind Error.   Rory Stark
• [BioC] plotpfm has been removed in PWMEnrich?   Robert Stojnic
• [BioC] plotpfm has been removed in PWMEnrich?   Robert Stojnic
• [BioC] plotpfm has been removed in PWMEnrich?   Robert Stojnic
• [BioC] plotpfm has been removed in PWMEnrich?   Robert Stojnic
• [BioC] RNA-Seq fold change compared to control, without replicates   Dario Strbenac
• [BioC] GAGE analysis   Roopa Subbaiaih
• [BioC] edgeR   Bogdan Tanasa
• [BioC] edgeR   Bogdan Tanasa
• [BioC] SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.   Tarca, Adi
• [BioC] processing BamFiles - streaming vs not streaming   Stefanie Tauber
• [BioC] failed to install biocondoctuor   Dan Tenenbaum
• [BioC] failed to install biocondoctuor   Dan Tenenbaum
• [BioC] Rsamtools installation error   Dan Tenenbaum
• [BioC] SNPstats package bug report   Dan Tenenbaum
• [BioC] SNPstats package bug report   Dan Tenenbaum
• [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation   Dan Tenenbaum
• [BioC] Using the devel Version of Bioconductor   Dan Tenenbaum
• [BioC] install pasilla   Dan Tenenbaum
• [BioC] Regarding R Package   Dan Tenenbaum
• [BioC] GLAD crashes when built with gcc-4.8   Dan Tenenbaum
• [BioC] Testing main effects and interactions in edgeR without contrasts   Ryan C. Thompson
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Ryan C. Thompson
• [BioC] Easy way to convert CharacterList to character, collapsing each element?   Ryan C. Thompson
• [BioC] Importing RMA processed data into limma for eBayes   Thornton, Matthew
• [BioC] Importing RMA processed data into limma for eBayes   Thornton, Matthew
• [BioC] BSmooth install question   Tim Triche, Jr.
• [BioC] minfi release 1.8   Elmar Tobi
• [BioC] minfi release 1.8   Elmar Tobi
• [BioC] tracks() and plotIdeogram() with non desired results in ggbio 1.10.9   Leonardo Collado Torres
• [BioC] Using Biostring to make position frequency matrix   Fabrice Tourre
• [BioC] Using Biostring to make position frequency matrix   Fabrice Tourre
• [BioC] plotpfm has been removed in PWMEnrich?   Fabrice Tourre
• [BioC] Change chars ACGT to ACGU in seqLogo   Fabrice Tourre
• [BioC] plotpfm has been removed in PWMEnrich?   Fabrice Tourre
• [BioC] plotpfm has been removed in PWMEnrich?   Fabrice Tourre
• [BioC] plotpfm has been removed in PWMEnrich?   Fabrice Tourre
• [BioC] plotpfm has been removed in PWMEnrich?   Fabrice Tourre
• [BioC] kmer and zscore calculation   Fabrice Tourre
• [BioC] kmer and zscore calculation   Fabrice Tourre
• [BioC] kmer and zscore calculation   Fabrice Tourre
• [BioC] Multiple contrasts in DESeq2   Hugo Varet
• [BioC] Multiple contrasts in DESeq2   Hugo Varet
• [BioC] Question about MEDIPS extend parameter   Vining, Kelly
• [BioC] Question about MEDIPS extend parameter   Vining, Kelly
• [BioC] using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] It works: RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS   Vining, Kelly
• [BioC] Dealing with probes with high fold change but PA call 0   Gundala Viswanath
• [BioC] Dealing with probes with high fold change but PA call 0   Gundala Viswanath
• [BioC] Why daisy() in cluster library failed to exclude NA when computing dissimilarity   Gundala Viswanath
• [BioC] scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"   Levi Waldron
• [BioC] Redundant gene sets & gagePipe   Luo Weijun
• [BioC] Can gage not use large gene sets for pathway analysis?   Luo Weijun
• [BioC] operations are possible only for numeric, logical or complex types   Luo Weijun
• [BioC] Rgraphviz installation issue   Luo Weijun
• [BioC] GAGE analysis   Luo Weijun
• [BioC] Analysing Affy data with limma   January Weiner
• [BioC] Analysing Affy data with limma   January Weiner
• [BioC] Gene shaving for bioconductor?   January Weiner
• [BioC] [R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x   David Winsemius
• [BioC] [R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x   David Winsemius
• [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?   Zhi-Qiang Ye
• [BioC] ggbio tracks with labelled: problem when I add a main title   Tengfei Yin
• [BioC] tracks() and plotIdeogram() with non desired results in ggbio 1.10.9   Tengfei Yin
• [BioC] subset a RleList using GRanges object?   Janet Young
• [BioC] subset a RleList using GRanges object?   Janet Young
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Janet Young
• [BioC] ggbio tracks with labelled: problem when I add a main title   Janet Young
• [BioC] ggbio tracks with labelled: problem when I add a main title   Janet Young
• [BioC] Why the resuts are so different between the classic and the glm methods?   Jiantao Yu
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Zhu, Lihua (Julie)
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Zhu, Lihua (Julie)
• [BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input   Zhu, Lihua (Julie)
• [BioC] Using the devel Version of Bioconductor   Zhu, Lihua (Julie)
• [BioC] Using the devel Version of Bioconductor   Zhu, Lihua (Julie)
• [BioC] Fwd: Annotation discrepancy   Eric Zollars
• [BioC] Annotation discrepancy HT HGU 133+ PM chip   Eric Zollars
• [BioC] Fwd: Annotation discrepancy   Eric Zollars
• [BioC] topGO spurious GO terms?   Adam [guest]
• [BioC] OMICtools: An informative directory for HTS and array analysis   Arnaud Desfeux [guest]
• [BioC] differential expression- edgeR   Ashutosh [guest]
• [BioC] edgeR question   Audra [guest]
• [BioC] calcNormFactors gives me NaN   Audra [guest]
• [BioC] calcNormFactors gives NaN normalization values- Please Help!   Audra [guest]
• [BioC] edge R exactTest output looks odd - PLEASE HELP!   Audra [guest]
• [BioC] XCMS for LC-MS   Bashar Amer [guest]
• [BioC] Install older version of Bioconductor   Dan Sullivan [guest]
• [BioC] Testing main effects and interactions in edgeR without contrasts   David Shuker [guest]
• [BioC] which genes to choose for being truly differentially expressed from a long list   EJ [guest]
• [BioC] Fitting linear model with different design matrix for each gene in limma   Elif Sarinay [guest]
• [BioC] Can DESeq2 find tissue-specific expression genes   Eman Lee [guest]
• [BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable erroR   Eugene Bolotin [guest]
• [BioC] Separating gene filtering and multiple testing p-value adjustment steps   FeiYian Yoon [guest]
• [BioC] FDR and Estimated Fragment length   George Harris [guest]
• [BioC] DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments   Gilgi [guest]
• [BioC] DESeq(normalize using all samples?)   Hui Zhao [guest]
• [BioC] DESeq2(analysis without replicate)   Hui Zhao [guest]
• [BioC] SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.   Ilario De Toma [guest]
• [BioC] mulitfactorial analysis, adjusting for quantitative covariates   Ingrid Dahlman [guest]
• [BioC] edgeR DGEList   Jahn Davik [guest]
• [BioC] time series data edgeR?   Jahn Davik [guest]
• [BioC] edgeR   Jahn Davik [guest]
• [BioC] edgeR glmFit   Jahn Davik [guest]
• [BioC] Apply non-Gaussian distribution data to limma   Jiang [guest]
• [BioC] makeTranscriptDbFromGFF finished successfully or not?   Jing [guest]
• [BioC] What software packages for Affymetrix HTA_2.0   Jinsheng Yu [guest]
• [BioC] limma2annaffy   Jose Lopez [guest]
• [BioC] Using \"model.matrix(~0 + as.factor(cancer), data=pheno)\" with \'sva\' package   Kaj Chokeshaiusaha [guest]
• [BioC] edgeR prior.count   Karen [guest]
• [BioC] SNPstats package bug report   LF [guest]
• [BioC] SNPstats package bug report   LF [guest]
• [BioC] operations are possible only for numeric, logical or complex types   Linda [guest]
• [BioC] forgeSeqFiles   Melo [guest]
• [BioC] Using a countDataSet as input data in DESeq2   Natalia [guest]
• [BioC] cooksCutoff error   Natalia [guest]
• [BioC] How do I remove bad samples/probes before normalization and SWAN?   Qin [guest]
• [BioC] Can gage not use large gene sets for pathway analysis?   Richard [guest]
• [BioC] affyPLM crashing R   Scott Robinson [guest]
• [BioC] Package SomaticCancerAlterations, import own .maf file?   Shila Ghazanfar [guest]
• [BioC] matchPattern vmatchPattern vectorised   Stephen [guest]
• [BioC] Pairwise Alignment on Large Protein Sequence Data Set   Thomas Atanasov [guest]
• [BioC] substr on XStringSet-class   Tim Homan [guest]
• [BioC] DESeq problem   abhishek singh chauhan [guest]
• [BioC] DB PROBLEM   abhishek singh chauhan [guest]
• [BioC] Oryza sativa problem   abhishek singh chauhan [guest]
• [BioC] (adj.p.value & log2FC) or (B.value & log2FC)   deb [guest]
• [BioC] prefiltering genelist before LIMMA & cut-off paramter for getting DEGs from topT object.   deb [guest]
• [BioC] hoeffd function (CRAN HMisc package) use in arrayQualityMetrics   jerry davison [guest]
• [BioC] install geneplotter   liyue [guest]
• [BioC] install pasilla   liyue [guest]
• package â pasillaâ is not available (for R version 3.0.2)   liyue [guest]
• [BioC] Issue installing rhdf5 package on R-3.0.2   shivali [guest]
• [BioC] Meta data for gene from GEO   rohan bareja
• [BioC] Fw: Meta data for gene from GEO   rohan bareja
• [BioC] Case vs Control Information,Diseases   rohan bareja
• [BioC] Case vs Control Information,Diseases   rohan bareja
• [BioC] time series data edgeR?   sh. chunxuan
• [BioC] annotation package for HuEx-1_0-st-v1 platform instead of pd.huex.1.0.st.v1   cstrato
• [BioC] Fwd: (adj.p.value & log2FC) or (B.value & log2FC)   debatosh das
• [BioC] Issue installing rhdf5 package on R-3.0.2   shivali gangwar
• [BioC] Issue installing rhdf5 package on R-3.0.2   shivali gangwar
• [BioC] Issue installing rhdf5 package on R-3.0.2   shivali gangwar
• [BioC] Fake Conferences CSCI and WORLDCOMP of Hamid Arabnia   rickardbrown at hushmail.com
• [BioC] remove evidence Codes   jfertaj
• [BioC] Rgraphviz installation issue   km
• [BioC] Rgraphviz installation issue   km
• [BioC] BSmooth install question   liwei_epi
• [BioC] Error in virtualArray Please help   Manvendra.Singh at mdc-berlin.de
• [BioC] About bandwidth in bkde2D   Asma rabe
• [BioC] Rsamtools installation error   nishant thakur
• [BioC] Best way to capture both NCBI and UCSC labeled alignments?   chris warth
• [BioC] R course in Boston December 19-20   sue at xlsolutions-corp.com
• [BioC] Regarding R Package   «Jαyαηth¡.A»

Last message date: Tue Dec 31 22:47:47 CET 2013
Archived on: Tue Dec 31 22:48:02 CET 2013

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