November 2013 Archives by subject

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Starting: Fri Nov 1 01:03:22 CET 2013
Ending: Sat Nov 30 14:08:37 CET 2013
Messages: 554

• [BioC] 2d loess   mahshid eskandari [guest]
• [BioC] 2d loess   Vincent Carey
• [BioC] [limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes   Jérôme Lane
• [BioC] [limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes   Gordon K Smyth
• [BioC] [limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes   Jérôme Lane
• [BioC] Adding logFC values to a custom annotation TopGO object   Bernardo Bello
• [BioC] Affymetrix HTA 2 array analysis   Stephen Turner
• [BioC] Affymetrix HTA 2 array analysis   Benilton Carvalho
• [BioC] agi4x44kpreprocess: `GEhelp` and `Treatment` variables   Stephen Hwang
• [BioC] agi4x44kpreprocess: `GEhelp` and `Treatment` variables   James W. MacDonald
• [BioC] agi4x44kpreprocess: `GEhelp` and `Treatment` variables   James W. MacDonald
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   María Maqueda [guest]
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   James W. MacDonald
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   María Maqueda González
• [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays   James W. MacDonald
• [BioC] Analysis of Human Gene 1.1 ST Array   Jerry Cholo
• [BioC] Analysis of Human Gene 1.1 ST Array   James W. MacDonald
• [BioC] Annotate - gene name to ENSEMBL   Kripa R
• [BioC] Annotate - gene name to ENSEMBL   Hans-Rudolf Hotz
• [BioC] Annotate - gene name to ENSEMBL   Marc Carlson
• [BioC] AnnotationHub resource down?   James W. MacDonald
• [BioC] AnnotationHub resource down?   Dan Tenenbaum
• [BioC] APE package on phylogenetic tree plot   guest [guest]
• [BioC] A question for QuasR::qQCReport   Michael Stadler
• [BioC] autoplot() error on a GRanges object in ggbio 1.10.8   Leonardo Collado Torres
• [BioC] autoplot() error on a GRanges object in ggbio 1.10.8   Tengfei Yin
• [BioC] autoplot() error on a GRanges object in ggbio 1.10.8   Tengfei Yin
• [BioC] autoplot() error on a GRanges object in ggbio 1.10.8   Leonardo Collado Torres
• [BioC] autoplot transcriptDb error with some regions   Cook, Malcolm
• [BioC] autoplot transcriptDb error with some regions   Tengfei Yin
• [BioC] autoplot transcriptDb error with some regions   Tengfei Yin
• [BioC] AWS / Bioconductor bug   Jason Miller
• [BioC] AWS / Bioconductor bug   Dan Tenenbaum
• [BioC] Bioconductor CMA PLS DA   liz considine [guest]
• [BioC] biomaRt : cannot useMart with biomart.informatics.jax.org because host="lindon"   Michael Love
• [BioC] biomaRt : cannot useMart with biomart.informatics.jax.org because host="lindon"   Steffen Durinck
• [BioC] biomaRt : cannot useMart with biomart.informatics.jax.org because host="lindon"   Michael Love
• [BioC] BSgenome.Mmulatta.UCSC   Brian Smith
• [BioC] BSgenome.Mmulatta.UCSC   Martin Morgan
• [BioC] BSgenome.Mmulatta.UCSC   Brian Smith
• [BioC] BSgenome.Mmulatta.UCSC   Martin Morgan
• [BioC] BSgenome.Mmulatta.UCSC   Brian Smith
• [BioC] BSgenome.Mmulatta.UCSC   Martin Morgan
• [BioC] BSgenome.Mmulatta.UCSC   Brian Smith
• [BioC] BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.   Diego Diez
• [BioC] BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.   Hervé Pagès
• [BioC] BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.   Diego Diez
• [BioC] Bug in GenomicRanges 1.14.3, as(from, "GRanges") not working for RleViewsList   George Baskozos
• [BioC] Bug in GenomicRanges 1.14.3, as(from, "GRanges") not working for RleViewsList   Hervé Pagès
• [BioC] Bug in GenomicRanges 1.14.3, as(from, "GRanges") not working for RleViewsList   George Baskozos
• [BioC] bug in graph::addNode() w/ graph::edgeData()   Robert Castelo
• [BioC] bug in graph::addNode() w/ graph::edgeData()   Paul Shannon
• [BioC] bug in graph::addNode() w/ graph::edgeData()   Robert Castelo
• [BioC] Building GenomicRanges1.14.3 on Centos6   Horne, Nigel (NIH/NLM/NCBI) [C]
• [BioC] Building GenomicRanges1.14.3 on Centos6   Sean Davis
• [BioC] Building GenomicRanges1.14.3 on Centos6   Horne, Nigel (NIH/NLM/NCBI) [C]
• [BioC] Building GenomicRanges1.14.3 on Centos6   Sean Davis
• [BioC] Calculating quantiles from very long Rle's that need to be aggregated   Leonardo Collado Torres
• [BioC] Calculating quantiles from very long Rle's that need to be aggregated   Michael Lawrence
• [BioC] Calculating quantiles from very long Rle's that need to be aggregated   Leonardo Collado Torres
• [BioC] change Gviz point size?   shao chunxuan
• [BioC] change Gviz point size?   James W. MacDonald
• [BioC] change Gviz point size?   shao chunxuan
• [BioC] clustering with already generated similarity matrix   Alyaa Mahmoud
• [BioC] Combat   Kovyrshina, Tatiana
• [BioC] Combat   Peter Langfelder
• [BioC] combination of frma, combat and barcode methods   Martinez.Raquel
• [BioC] combination of frma, combat and barcode methods   Matthew McCall
• [BioC] confused with edgeR: multiple groups vs one control   Joel Rodriguez-Medina [guest]
• [BioC] confused with edgeR: multiple groups vs one control   Mark Robinson
• [BioC] Construct design matrix for qPCR data using Limma package   Hongda Chen
• [BioC] Construct design matrix for qPCR data using Limma package   Hongda Chen
• [BioC] Construct design matrix for qPCR data using Limma package   James W. MacDonald
• [BioC] Count outlier detection and endogenous gene normalization   FeiYian Yoong [guest]
• [BioC] Count outlier detection and endogenous gene normalization   Michael Love
• [BioC] Create a sample file /tab delimited file in QuasR   Michael Stadler
• [BioC] Cross map two different probe set IDs   Jerry Cholo
• [BioC] Cross map two different probe set IDs   Tim Triche, Jr.
• [BioC] Cross map two different probe set IDs   Jerry Cholo
• [BioC] Cross map two different probe set IDs   Marc Carlson
• [BioC] DEG Calling on Transcripts vs Genes   Yogesh Saletore
• [BioC] DESeq2 : NA p values reported   Abhishek Pratap
• [BioC] DESeq2 : NA p values reported   Michael Love
• [BioC] DESeq2; FoldChange values with only 0's   Hanneke van Deutekom
• [BioC] DESeq2; FoldChange values with only 0's   Michael Love
• [BioC] DESeq2; FoldChange values with only 0's   Michael Love
• [BioC] DESeq2; FoldChange values with only 0's   Michael Love
• [BioC] DESeq2 multifactorial formula   Ugo Borello
• [BioC] DESeq2 multifactorial formula   Michael Love
• [BioC] DESeq2 multifactorial formula   Ugo Borello
• [BioC] DESeq2 with GAGE   Luo Weijun
• [BioC] DESeq: normalizing additional sample to already normalized set of samples   Dorota Herman
• [BioC] DESeq: normalizing additional sample to already normalized set of samples   Michael Love
• [BioC] DESeq: normalizing additional sample to already normalized set of samples   Dorota Herman
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Lucia Peixoto
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Michael Love
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Rory Stark
• [BioC] DEseq for chip-seq data normalisation   Davide Cittaro
• [BioC] DEseq for chip-seq data normalisation   pbczyd .
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Rory Stark
• [BioC] DEseq for chip-seq data normalisation   Giuseppe Gallone
• [BioC] DEseq for chip-seq data normalisation   Ying Wu
• [BioC] DEseq for chip-seq data normalisation   Rory Stark
• [BioC] DEseq for chip-seq data normalisation   Ying Wu
• [BioC] DEseq for chip-seq data normalisation   Ryan
• [BioC] DESeq nbinomGLMTest specific comparisons   James Floyd
• [BioC] DESeq nbinomGLMTest specific comparisons   Steve Lianoglou
• [BioC] DESeq warning: "Dispersion fit did not converge" with replicates counts data   Jiewencai
• [BioC] DESeq warning: "Dispersion fit did not converge" with replicates counts data   Michael Love
• [BioC] DEXSeq, gene not testable due to 2 out of 84 exons with a low nr of counts   Hanneke van Deutekom
• [BioC] DEXSeq, gene not testable due to 2 out of 84 exons with a low nr of counts   Simon Anders
• [BioC] Dexseq package: dexseq_count error message and warnings   capricy gao
• [BioC] Dexseq package: dexseq_count error message and warnings   Alejandro Reyes
• [BioC] Dexseq package: dexseq_count error message and warnings   capricy gao
• [BioC] Dexseq package: dexseq_count error message and warnings   Alejandro Reyes
• [BioC] Dexseq package: dexseq_count error message and warnings   capricy gao
• [BioC] Dexseq package: dexseq_count error message and warnings   Simon Anders
• [BioC] Dexseq package: dexseq_count error message and warnings   Sean Davis
• [BioC] Dexseq package: dexseq_count error message and warnings   capricy gao
• [BioC] Dexseq package: dexseq_count error message and warnings   Alejandro Reyes
• [BioC] Dexseq package: looking for help with function -- newExonCountSet()   capricy gao
• [BioC] Dexseq package: looking for help with function -- newExonCountSet()   Alejandro Reyes
• [BioC] Dexseq package: looking for help with function -- newExonCountSet()   capricy gao
• [BioC] DEXSeq package: plotDEXSeq for multiple conditions   capricy gao
• [BioC] DEXSeq package: plotDEXSeq for multiple conditions   Alejandro Reyes
• [BioC] DEXSeq package: plotDEXSeq for multiple conditions   capricy gao
• [BioC] DiffBind - error when setting manual contrast groups   Giuseppe Gallone
• [BioC] DiffBind - Info   Rory Stark
• [BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap   Matt Zinkgraf [guest]
• [BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap   Rory Stark
• [BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap   Rory Stark
• [BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap   Matt Zinkgraf
• [BioC] Differential expression of RNA-seq data using limma and voom()   Jon Bråte
• [BioC] Differential expression of RNA-seq data using limma and voom()   Michael Love
• [BioC] Differential expression of RNA-seq data using limma and voom()   Gordon K Smyth
• [BioC] Differential gene expression of a cluster or group of genes   January Weiner
• [BioC] Differential gene expression of a cluster or group of genes   Gordon K Smyth
• [BioC] distribution of agilent array data.   shao chunxuan
• [BioC] distribution of agilent array data.‏   shao chunxuan
• [BioC] distribution of agilent array data.‏   James W. MacDonald
• [BioC] distribution of agilent array data.‏   shao chunxuan
• [BioC] distribution of agilent array data.‏   Mayer, Claus-Dieter
• [BioC] distribution of agilent array data.‏   shao chunxuan
• [BioC] easyRNAseq and DEseq for no replicate RNAseq   Isabelle Stévant
• [BioC] easyRNAseq and DEseq for no replicate RNAseq   Nicolas Delhomme
• [BioC] easyRNAseq and DEseq for no replicate RNAseq   Nicolas Delhomme
• [BioC] easyRNASeq for miRNA read counts   Vicky Chu [guest]
• [BioC] easyRNASeq for miRNA read counts   Nicolas Delhomme
• [BioC] easyRNASeq for miRNA read counts   Nicolas Delhomme
• [BioC] edgeR - 3-dimensional Multidimensional scaling   Paraskevas Iatropoulos
• [BioC] edgeR - 3-dimensional Multidimensional scaling   Mark Robinson
• [BioC] edgeR - 3-dimensional Multidimensional scaling   Paraskevas Iatropoulos
• [BioC] edgeR on ncRNA analysis question   alessandro.guffanti at genomnia.com
• [BioC] Error: All the CEL files must be of the same type   Jerry Cholo
• [BioC] Error: All the CEL files must be of the same type   James W. MacDonald
• [BioC] Error in gzfile(fname, open = “rt”) : invalid 'description' argument   水静流深
• [BioC] Error in gzfile(fname, open = “rt”) : invalid 'description' argument - GEOquery   Dan Du
• [BioC] Error in gzfile(fname, open = “rt”) : invalid 'description' argument - GEOquery   Sean Davis
• [BioC] Excluding probes during methylation analysis   Victoria Svinti
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Hans-Rudolf Hotz
• [BioC] exon genomic coordinates   Michael Lawrence
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Martin Morgan
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Martin Morgan
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Michael Lawrence
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Michael Lawrence
• [BioC] exon genomic coordinates   array chip
• [BioC] exon genomic coordinates   Hervé Pagès
• [BioC] exon genomic coordinates   array chip
• [BioC] ExpressionSet error message: "featureNames differ"   Jobin K. Varughese
• [BioC] ExpressionSet error message: "featureNames differ"   Steve Lianoglou
• [BioC] ExpressionSet error message: "featureNames differ"   Jobin K. Varughese
• [BioC] ExpressionSet error message: "featureNames differ"   Martin Morgan
• [BioC] ExpressionSet error message: "featureNames differ"   Jobin K. Varughese
• [BioC] Farms/Call.INI using oligo package?   Fraser Sim
• [BioC] Farms/Call.INI using oligo package?   cstrato
• [BioC] Farms/Call.INI using oligo package?   Djork-Arné Clevert
• [BioC] Farms/Call.INI using oligo package?   Djork-Arné Clevert
• [BioC] Farms/Call.INI using oligo package?   Fraser Sim
• [BioC] Farms/Call.INI using oligo package?   Djork-Arné Clevert
• [BioC] Finding similarities between multiple sequenced genomic libraries   Gordon [guest]
• [BioC] Finding similarities between multiple sequenced genomic libraries   Ryan
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Nicolas Delhomme
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Michael Lawrence
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Nicolas Delhomme
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Michael Lawrence
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Hervé Pagès
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Hervé Pagès
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Michael Lawrence
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Nicolas Delhomme
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Michael Lawrence
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Hervé Pagès
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Hervé Pagès
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Nicolas Delhomme
• [BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?   Michael Lawrence
• [BioC] flowCore transformation function   Mike
• [BioC] FRiP for ChIP-seq in Bioconductor?   Sidders, Benjamin
• [BioC] FRiP for ChIP-seq in Bioconductor?   Giuseppe Gallone
• [BioC] FRiP for ChIP-seq in Bioconductor?   Rory Stark
• [BioC] Fwd: [devteam-bioc] information about genefilter package   Hervé Pagès
• [BioC] Fwd: [devteam-bioc] information about genefilter package   James W. MacDonald
• [BioC] gage function---kegg.gsets   Richard [guest]
• [BioC] gage function---kegg.gsets   Luo Weijun
• [BioC] Gene filtering for RNA-seq data   FeiYian Yoong [guest]
• [BioC] Gene filtering for RNA-seq data   Michael Love
• [BioC] Gene filtering for RNA-seq data   Tim Triche, Jr.
• [BioC] Generating GEO submission files from beadarray summary data   Kemal Akat
• [BioC] Generating GEO submission files from beadarray summary data   Aliaksei Holik
• [BioC] Generating GEO submission files from beadarray summary data   Kemal Akat
• [BioC] Generating GEO submission files from beadarray summary data   Mark Dunning
• [BioC] Generating GEO submission files from beadarray summary data   Aliaksei Holik
• [BioC] Generating GEO submission files from beadarray summary data   Mark Dunning
• [BioC] Generating GEO submission files from beadarray summary data   Kemal Akat
• [BioC] Generating GEO submission files from beadarray summary data   Aliaksei Holik
• [BioC] getAnnMap: package hugene10stv1 not available   Claudia [guest]
• [BioC] getAnnMap: package hugene10stv1 not available   Vincent Carey
• [BioC] getAnnMap: package hugene10stv1 not available   Claudia
• [BioC] GGally ggbio conflict/bug   Paulson, Ariel
• [BioC] GGally ggbio conflict/bug   Michael Lawrence
• [BioC] GGally ggbio conflict/bug   Cook, Malcolm
• [BioC] GGally ggbio conflict/bug   Barret Schloerke
• [BioC] GGally ggbio conflict/bug   Tengfei Yin
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Leonardo Collado Torres
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Tengfei Yin
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Tengfei Yin
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Leonardo Collado Torres
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Leonardo Collado Torres
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Tengfei Yin
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Leonardo Collado Torres
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Tengfei Yin
• [BioC] ggbio::plotIdeogram() not working on R 3.0.2   Leonardo Collado Torres
• [BioC] GOSemSim function, clusterSim throws expired SQLiteConnection error   Gabriel [guest]
• [BioC] GOSemSim function, clusterSim throws expired SQLiteConnection error   Guangchuang Yu
• [BioC] GRanges Overlaps   Giovanni Carosso
• [BioC] GRanges Overlaps   Tim Triche, Jr.
• [BioC] GRanges Overlaps   Michael Lawrence
• [BioC] GRanges Overlaps   Tim Triche, Jr.
• [BioC] GRanges Overlaps   Giovanni Carosso
• [BioC] GRanges Overlaps   Michael Lawrence
• [BioC] GRanges Overlaps   Giovanni Carosso
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Tim Smith
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Dario Strbenac
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Tim Smith
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Dario Strbenac
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Tim Smith
• [BioC] Graph of methylation data around TSS - Repitools or other package?   Dario Strbenac
• [BioC] GSEABase error parsing msigdb_v4.0.xml   Milica Ng
• [BioC] GSEABase error parsing msigdb_v4.0.xml   Martin Morgan
• [BioC] GTF file error when using easyRNAseq   Nicolas Delhomme
• [BioC] GTF file error when using easyRNAseq   Nicolas Delhomme
• [BioC] GTF file error when using easyRNAseq   Michael Lawrence
• [BioC] GTF file error when using easyRNAseq   Nicolas Delhomme
• [BioC] GTF file error when using easyRNAseq   Michael Lawrence
• [BioC] GTF file error when using easyRNAseq   Natalia Sevane
• [BioC] GTF file error when using easyRNAseq   Nicolas Delhomme
• GTF file error when using easyRNAseqâ   Natalia [guest]
• [BioC] Gviz - show plus and minus strand from a bam   António domingues
• [BioC] Gviz - show plus and minus strand from a bam   Hahne, Florian
• [BioC] Gviz - show plus and minus strand from a bam   António domingues
• [BioC] Gviz and Leishmania genomes   Hahne, Florian
• [BioC] heatmap.2 - change column & row locations; angle / rotate   Cheng, Yong-Sheng
• [BioC] help: goseq and makeOrgPackageFromNCBI in AnnotationForge   刘鹏飞
• [BioC] help: goseq and makeOrgPackageFromNCBI in AnnotationForge   Marc Carlson
• [BioC] Help on sapply() with GRanges   Prashantha Hebbar
• [BioC] Help on sapply() with GRanges   James W. MacDonald
• [BioC] Help on sapply() with GRanges   Michael Lawrence
• [BioC] help with SCAN.UPC and u133aaofav2   Juliet Hannah
• [BioC] help with SCAN.UPC and u133aaofav2   Steve Piccolo
• [BioC] help with SCAN.UPC and u133aaofav2   Juliet Hannah
• [BioC] help with SCAN.UPC and u133aaofav2   Steve Piccolo
• [BioC] High intensity probes might cause problems   Aileen Chefai
• [BioC] How to analyze my hg 1.1 st array   Jerry Cholo
• [BioC] How to analyze my hg 1.1 st array   James W. MacDonald
• [BioC] How to compare GO term lists and create matching network?   Bernardo Bello
• [BioC] How to compare GO term lists and create matching network?   Paul Shannon
• [BioC] how to get Entrez Gene ID from genomic coordinates   Bruna Marini
• [BioC] how to get Entrez Gene ID from genomic coordinates   James W. MacDonald
• [BioC] how to make transcript db from ucsc for mm8   Ou, Jianhong
• [BioC] how to make transcript db from ucsc for mm8   Hervé Pagès
• [BioC] how to make transcript db from ucsc for mm8   Ou, Jianhong
• [BioC] How to save the result from calling matchPWM?   Yisong Zhen
• [BioC] How to save the result from calling matchPWM?   Hervé Pagès
• [BioC] HTqPCR normalization issues - third posting   alessandro.guffanti at genomnia.com
• [BioC] HTqPCR normalization issues - third posting   Levi Waldron
• [BioC] HTqPCR normalization issues - third posting   alessandro.guffanti at genomnia.com
• [BioC] HTqPCR normalization issues - third posting   Levi Waldron
• [BioC] HTqPCR normalization issues - third posting   alessandro.guffanti at genomnia.com
• [BioC] Human Gene 1.1 st array   Jerry Cholo
• [BioC] Hypergeometric test   amit kumar subudhi
• [BioC] Hypergeometric test   Steve Lianoglou
• [BioC] Illumina Expression analysis from iDAT files   Sean Davis
• [BioC] Illumina Expression analysis from iDAT files   Mike Smith
• [BioC] Illumina Expression analysis from iDAT files   Sean Davis
• [BioC] Illumina Expression analysis from iDAT files   Gordon K Smyth
• [BioC] Illumina Expression analysis from iDAT files   Mike Smith
• [BioC] Illumina Expression analysis from iDAT files   Sean Davis
• [BioC] Illumina Expression analysis from iDAT files   Tim Triche, Jr.
• [BioC] Improve Bioconductor mailing list with tags   Bernardo Bello
• [BioC] Improve Bioconductor mailing list with tags   Martin Morgan
• [BioC] Improve Bioconductor mailing list with tags   Bernardo Bello
• [BioC] inconsistency in illuminaHumanv4.db?   P.D. Moerland
• [BioC] inconsistency in illuminaHumanv4.db?   Mark Dunning
• [BioC] incorrect number of dimensions   Jason [guest]
• [BioC] incorrect number of dimensions   Steve Lianoglou
• [BioC] Inquiries about fitType on DESeq2   Michael Love
• [BioC] Interpretation Fold Change - Limma   Christian De Santis
• [BioC] Interpretation Fold Change - Limma   Pekka Kohonen
• [BioC] Isobar module   Trinidad Martín Campos
• [BioC] Isobar module   Dan Tenenbaum
• [BioC] Isobar module   Dan Tenenbaum
• [BioC] Job in statistical genetics / bioinformatics   Paul Leo
• [BioC] Limma, blocking, robust methods, and paired samples question   Gustavo Fernandez Bayon
• [BioC] Limma, blocking, robust methods, and paired samples question   Gordon K Smyth
• [BioC] Limma, blocking, robust methods, and paired samples question   Gordon K Smyth
• [BioC] Limma, blocking, robust methods, and paired samples question   Tim Triche, Jr.
• [BioC] limma - genas: unexpected warnings   Hooiveld, Guido
• [BioC] Limma and pre processing Agilent single color arrays   amandafassis at usp.br
• [BioC] Limma and pre processing Agilent single color arrays   gregory voisin
• [BioC] Limma and pre processing Agilent single color arrays   Gordon K Smyth
• [BioC] limma duplicateCorrelation - unbalanced paired design   Sarah Bonnin
• [BioC] Limma for DNA methylation arrays?   Gordon K Smyth
• [BioC] LIMMA on RT-PCR data   Sandhya Pemmasani Kiran
• [BioC] LIMMA on RT-PCR data   Ryan
• [BioC] LIMMA on RT-PCR data   MSU_JPS
• [BioC] LIMMA on RT-PCR data   Gordon K Smyth
• [BioC] LIMMA on RT-PCR data   Ryan
• [BioC] LIMMA on RT-PCR data   Gordon K Smyth
• [BioC] LIMMA on RT-PCR data   Sandhya Pemmasani Kiran
• [BioC] Limma with homemade chip, multiple probes per gene, no replicates?   Gordon [guest]
• [BioC] Limma with homemade chip, multiple probes per gene, no replicates?   Gordon K Smyth
• [BioC] lmFit: Error in dimnames(fit$cov.coefficients)   Mete Civelek
• [BioC] lmFit: Error in dimnames(fit$cov.coefficients)   Gordon K Smyth
• [BioC] lmFit: Error in dimnames(fit$cov.coefficients)   Mete Civelek
• [BioC] lmFit: Error in dimnames(fit$cov.coefficients)   Mete Civelek
• [BioC] Loading eSet.r objects from ArrayExpress   Maciej Jończyk
• [BioC] Metabolomic data analysis with papi / papiHtest() does not work as expected   Carsten Jaeger [guest]
• [BioC] Metabolomic data analysis with papi / papiHtest() does not work as expected   Aggio, Raphael
• [BioC] Metabolomic data analysis with papi / papiHtest() does not work as expected   Raphael Aggio
• [BioC] Metabolomic data analysis with papi / papiHtest() does not work as expected   Carsten Jaeger
• [BioC] Meta data for gene from GEO   Rohan [guest]
• [BioC] Meta data for gene from GEO   Sean Davis
• [BioC] Meta data for gene from GEO   rohan bareja
• [BioC] Meta data for gene from GEO   Sean Davis
• [BioC] Meta data for gene from GEO   rohan bareja
• [BioC] methyAnalysis error   Juan Fernandez
• [BioC] methyAnalysis error   jfertaj
• [BioC] methyAnalysis error   Pan Du
• [BioC] methyAnalysis error   Pan Du
• [BioC] methyAnalysis error   jfertaj
• [BioC] methyAnalysis error   Pan Du
• [BioC] methyAnalysis error   Martin Morgan
• [BioC] methyAnalysis error   Pan Du
• [BioC] MethyLumiM to MethyLumiSet?   Martin Rijlaarsdam
• [BioC] MethyLumiM to MethyLumiSet?   Tim Triche, Jr.
• [BioC] MethyLumiM to MethyLumiSet?   Allegra A. Petti
• [BioC] MethyLumiM to MethyLumiSet?   Martin Rijlaarsdam
• [BioC] MethyLumiM to MethyLumiSet?   Victoria Svinti
• [BioC] MethyLumiM to MethyLumiSet?   Tim Triche, Jr.
• [BioC] MethyLumiM to MethyLumiSet?   Allegra A. Petti
• [BioC] MethyLumiM to MethyLumiSet?   Victoria Svinti
• [BioC] MethyLumiM to MethyLumiSet?   Tim Triche, Jr.
• [BioC] MethyLumiM to MethyLumiSet?   Allegra A. Petti
• [BioC] minfi release 1.8   Kasper Daniel Hansen
• [BioC] minfi release 1.8   Elmar Tobi
• [BioC] New GO terms after TopGO enrichment? (updated)   Adrian Alexa
• [BioC] New GO terms after TopGO enrichment? (updated)   Bernardo Bello
• [BioC] New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)   Leo Lahti
• [BioC] Oligo package error   guest [guest]
• [BioC] Oligo package error   James W. MacDonald
• [BioC] On empirical Bayes of edgeR   Bin Zhuo [guest]
• [BioC] On empirical Bayes of edgeR   Gordon K Smyth
• [BioC] package built under R version 3.1.0 warning   Diego Diez
• [BioC] package built under R version 3.1.0 warning   Marc Carlson
• [BioC] package built under R version 3.1.0 warning   Diego Diez
• [BioC] pair-wise analysis of multifactorial design in DESeq   Assa Yeroslaviz
• [BioC] PAM-50 genefu example with Hu-133A GEO datasets   Peterson, Leif
• [BioC] PAM-50 genefu example with Hu-133A GEO datasets   Benjamin Haibe-Kains
• [BioC] pathview -- ID Problem?   Luo Weijun
• [BioC] pathview -- ID Problem?   fabian
• [BioC] pathview -- ID Problem?   Luo Weijun
• [BioC] plot QuSAGE problem   Natalia [guest]
• [BioC] plot QuSAGE problem   Chris Bolen
• [BioC] plot QuSAGE problem   Natalia Sevane
• [BioC] plot QuSAGE problem   Chris Bolen
• [BioC] Probe Set IDs and Gene Names for Human Gene 1.1 ST array   Shahla Ghaumipour
• [BioC] Probe Set IDs and Gene Names for Human Gene 1.1 ST array   James W. MacDonald
• [BioC] Problem with flowMerge   oscar Jottrand
• [BioC] Problem with GenomicRanges 1.14.3, as(from, \"GRanges\") not working for RleViewsList   Giorgos Baskozos [guest]
• [BioC] Problem with the oligo package for nimblegen analysis   William Oldham
• [BioC] Problem with topTable function (after Bioconductor update)   Gordon K Smyth
• [BioC] question about design for limma time course, 2 conditions and drug treatment microarray experiment   Ninni Nahm [guest]
• [BioC] question about design for limma time course, 2 conditions and drug treatment microarray experiment   Gordon K Smyth
• [BioC] question about design for limma time course, 2 conditions and drug treatment microarray experiment   Pekka Kohonen
• [BioC] question about design for limma time course, 2 conditions and drug treatment microarray experiment   Pekka Kohonen
• [BioC] Question about ReportingTools used with DESeq2   amandine.fournier at chu-lyon.fr
• [BioC] Question about ReportingTools used with DESeq2   James W. MacDonald
• [BioC] Question about ReportingTools used with DESeq2   Jason Hackney
• [BioC] question regarding the behavior of function processReads in package nucleR   Ulrike Goebel
• [BioC] Questions regarding 'specond' r-program library package   Florence Cavalli
• [BioC] Random effect for RNAseq data in Limma package   sci yasmin
• [BioC] Random effect for RNAseq data in Limma package   Gordon K Smyth
• [BioC] readVcf fails when ALT field contains breakends and no symbolic allele   Valerie Obenchain
• [BioC] readVcf fails when ALT field contains breakends and no symbolic allele   Daniel Cameron
• [BioC] readVcf fails when ALT field contains breakends and no symbolic allele   Valerie Obenchain
• [BioC] Redundant gene sets & gagePipe   Christian De Santis
• [BioC] ref : org.Hs.eg.db   Abhishek Pratap
• [BioC] ref : org.Hs.eg.db   Abhishek Pratap
• [BioC] ref : org.Hs.eg.db   Steve Lianoglou
• [BioC] RefSeq coordinates from biomaRt   Dave Tang
• [BioC] RefSeq coordinates from biomaRt   Sean Davis
• [BioC] RefSeq coordinates from biomaRt   Dave Tang
• [BioC] RefSeq coordinates from biomaRt   Sean Davis
• [BioC] RefSeq coordinates from biomaRt   Dave Tang
• [BioC] Reg : Package RDAVIDWebService not connecting to DAVID-WS   Fazulur Rehaman
• [BioC] Reg : Package RDAVIDWebService not connecting to DAVID-WS   Fazulur Rehaman
• [BioC] Reg : Package RDAVIDWebService not connecting to DAVID-WS   gregory voisin
• [BioC] Reg : Package RDAVIDWebService not connecting to DAVID-WS   Cristobal Fresno Rodríguez
• [BioC] Reg : Package RDAVIDWebService not connecting to DAVID-WS   Fazulur Rehaman
• [BioC] Releases of DESeq2   amandine.fournier at chu-lyon.fr
• [BioC] Releases of DESeq2   Michael Love
• [BioC] ReportingTools package   Jason Hackney
• [BioC] ReportingTools package   hena ramay
• [BioC] Retrieve GO terms for organism without complete genomes and do enrichment by myself   Ricardo Silva
• [BioC] Retrieve GO terms for organism without complete genomes and do enrichment by myself   Marc Carlson
• [BioC] Retrieve GO terms for unanontaded organism and do enrichment by myself   Ricardo Silva
• [BioC] retrieving annotation   Kathi Zarnack
• [BioC] retrieving annotation   Nicolas Delhomme
• [BioC] retrieving annotation   Hervé Pagès
• [BioC] retrieving annotation   Kathi Zarnack
• [BioC] retrieving annotation   Kathi Zarnack
• [BioC] Re： DESeq warning: "Dispersion fit did not converge" withreplicates counts data   Jiewencai
• [BioC] rhdf5, dataframes, and variable length strings   Bernd Fischer
• [BioC] rhdf5, dataframes, and variable length strings   Bernd Fischer
• [BioC] rhdf5 write/read inconsistency   Brad Friedman [guest]
• [BioC] rhdf5 write/read inconsistency   Julian Gehring
• [BioC] rhdf5 write/read inconsistency   Julian Gehring
• [BioC] rhdf5 write/read inconsistency   Bernd Fischer
• [BioC] RNAseq visualization tools   Claudio Isella
• [BioC] RNAseq visualization tools   Ryan
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Ryan C. Thompson
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Wei Shi
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Ryan
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Wei Shi
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Wei Shi
• [BioC] Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?   Ryan Thompson
• [BioC] rtrackleyer/GenomicRanges: How can I group GRanges by metadata attributes   chris warth [guest]
• [BioC] rtrackleyer/GenomicRanges: How can I group GRanges by metadata attributes   Michael Lawrence
• [BioC] SCAN.UPC for Illumina arrays?   Tim Triche, Jr.
• [BioC] SCAN.UPC for Illumina arrays?   Mark Dunning
• [BioC] SCAN.UPC for Illumina arrays?   Tim Triche, Jr.
• [BioC] SCAN.UPC for Illumina arrays?   Steve Piccolo
• [BioC] SCAN.UPC for Illumina arrays?   Mark Dunning
• [BioC] SCAN.UPC for Illumina arrays?   Tim Triche, Jr.
• [BioC] Separate channel analysis of two color micro arrays: avereps and intraspotCorrelation functions   Rob [guest]
• [BioC] Separate channel analysis of two color micro arrays:avereps and intraspotCorrelation functions   Gordon K Smyth
• [BioC] ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values   Sam McInturf
• [BioC] ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values   Martin Morgan
• [BioC] ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values   Sam McInturf
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Marcin Jakub Kamiński
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Gordon K Smyth
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Gordon K Smyth
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Marcin Jakub Kamiński
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Gordon K Smyth
• [BioC] Single-channel GenePix analysis with Limma (bg correction, normalization, weights)   Marcin Jakub Kamiński
• [BioC] stranded intronic variants with VariantAnnotation::locateVariants()   Valerie Obenchain
• [BioC] stranded intronic variants with VariantAnnotation::locateVariants()   Robert Castelo
• [BioC] strange layering in PCA after removeBatchEffect()   Julien Roux
• [BioC] strange layering in PCA after removeBatchEffect()   Julien Roux
• [BioC] strange layering in PCA after removeBatchEffect()   Gordon K Smyth
• [BioC] Summarisation in oligo package after exclusion of probes containing SNPs   Jimmy Peters [guest]
• [BioC] Summarisation in oligo package after exclusion of probes containing SNPs   Daniel Bottomly
• [BioC] Summarisation in oligo package after exclusion of probes containing SNPs   Dr J. Peters
• [BioC] Summarization by gene or exon or transcript   Michael Stadler
• [BioC] Summarization by gene or exon or transcript   Reema Singh
• [BioC] supraHex for tabular omics data analysis using a supra-hexagonal map   Hai Fang
• [BioC] supraHex for tabular omics data analysis using a supra-hexagonal map   Steve Lianoglou
• [BioC] tracks() and plotIdeogram() with non desired results in ggbio 1.10.9   Leonardo Collado Torres
• [BioC] tracks() and plotIdeogram() with non desired results in ggbio 1.10.9   Tengfei Yin
• [BioC] tracks() and plotIdeogram() with non desired results in ggbio 1.10.9   Leonardo Collado Torres
• [BioC] unable to install \"ALL\"   xia yuan [guest]
• [BioC] unable to install \"ALL\"   Dan Tenenbaum
• [BioC] unable to install \"ALL\"   Dan Tenenbaum
• [BioC] Unable to install hgu133plus2.db   Ellie McIntosh [guest]
• [BioC] unable to install package   ashok raja balla [guest]
• [BioC] unable to install package   Dan Tenenbaum
• [BioC] unable to install package   Martin Morgan
• [BioC] Unable to load xps...   Bas Jansen
• [BioC] Unable to load xps...   cstrato
• [BioC] use selectWeka() for feature selection   kai wang [guest]
• [BioC] Using changeLog() to see updates to limma package   Gordon K Smyth
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Sylvain Foisy
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Sylvain Foisy Ph. D.
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Nicolas Delhomme
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Sylvain Foisy Ph. D.
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Nicolas Delhomme
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Sylvain Foisy Ph. D.
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Martin Morgan
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Martin Morgan
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Nicolas Delhomme
• [BioC] Using easyRNASeq package: question about BAM/BAI and links to them   Nicolas Delhomme
• [BioC] Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data   Michael Love
• [BioC] Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data   Shucong Li
• [BioC] Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data   Shucong Li
• [BioC] Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data   Shucong Li
• [BioC] Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data   Michael Love
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Michael Lawrence
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Michael Lawrence
• [BioC] VariantTools: callVariants error   heyi xiao
• [BioC] VariantTools: callVariants error   Michael Lawrence
• [BioC] VariantTools: callVariants error   Hervé Pagès
• [BioC] VariantTools: callVariants error   heyi xiao
• [BioC] VariantTools callVariants - binomial likelihood ratio   heyi xiao
• [BioC] VariantTools callVariants - binomial likelihood ratio   Michael Lawrence
• [BioC] VariantTools callVariants - binomial likelihood ratio   heyi xiao
• [BioC] VariantTools callVariants - binomial likelihood ratio   Michael Lawrence
• [BioC] VariantTools installation problem: dependencies not available   heyi xiao
• [BioC] VariantTools installation problem: dependencies not available   Michael Lawrence
• [BioC] VariantTools installation problem: dependencies not available   heyi xiao
• [BioC] VariantTools installation problem: dependencies not available   Steve Lianoglou
• [BioC] VariantTools installation problem: dependencies not available   Martin Morgan
• [BioC] VariantTools installation problem: dependencies not available   heyi xiao
• [BioC] VariantTools installation problem: dependencies not available   Michael Lawrence
• [BioC] VariantTools installation problem: dependencies not available   heyi xiao
• [BioC] virtualArray: Error at second execution of virtualArrayExpressionSets   Adrian [guest]
• [BioC] Voom and CQN input   Heather Estrella
• [BioC] Voom and CQN input   Ryan
• [BioC] Voom and CQN input   Gordon K Smyth
• [BioC] Voom and CQN input   Gordon K Smyth
• [BioC] What packages needed for anti-correlated clustering?   Parth Patel
• [BioC] What packages needed for anti-correlated clustering?   Tim Triche, Jr.
• [BioC] What packages needed for anti-correlated clustering?   Peter Langfelder
• [BioC] What packages needed for anti-correlated clustering?   Tim Triche, Jr.
• [BioC] WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)   bach le
• [BioC] WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)   Michael Lawrence
• [BioC] WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)   bach le
• [BioC] WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)   Michael Lawrence
• [BioC] WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)   bach le
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Valerie Obenchain
• â SequenceAnalysisDataâ is not available   John [guest]
• [BioC] â SequenceAnalysisDataâ is not available   Dan Tenenbaum
• [BioC] â SequenceAnalysisDataâ is not available   John Miller

Last message date: Sat Nov 30 14:08:37 CET 2013
Archived on: Sat Nov 30 14:09:19 CET 2013

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