January 2012 Archives by author

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Starting: Sun Jan 1 00:19:06 CET 2012
Ending: Tue Jan 31 22:16:43 CET 2012
Messages: 449

• [BioC] R: how to get a list of the genes in each module in WGCNA   Manca Marco (PATH)
• [BioC] Please help! How to specify factors for a RCBD in edgeR   Tilahun Abebe
• [BioC] Bioconductor Digest, Vol 107, Issue 31   Tilahun Abebe
• [BioC] help with limma design,contrast matrix please   John Alexander
• [BioC] Two populations on microarray   Naomi Altman
• [BioC] Two populations on microarray   Naomi Altman
• [BioC] DESeq for an mRNA-seq time course   Simon Anders
• [BioC] DESeq: how to get the variance information   Simon Anders
• [BioC] how edgeR control the outliers?   Simon Anders
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Cory Barr
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Cory Barr
• [BioC] Installing bioconductor with openSUSE 11.4 and R 2.14   Bartlett, Thomas
• [BioC] OpenSuse 11.4, cannot install Bioconductor due to missing C compiler   Tom Bartlett
• [BioC] displaying clustering results in TreeView or MapleTree   Mark Baumeister
• [BioC] converting intensity values to log ratios?   Mark Baumeister
• [BioC] mergeScans function in limma - minFactor error   Henrik Bengtsson
• [BioC] Help With RNA-seq   Tina Asante Boahene
• [BioC] Help With RNA-seq   Tina Asante Boahene
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Ben Bolstad
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Ben Bolstad
• [BioC] probability of a point membership to a certain cluster   Hector Corrada Bravo
• [BioC] RMA normalisation of test microarray data to training data   Daniel Brewer
• [BioC] DESeq - ChIP-seq (including background reads)   Gordon Brown
• [BioC] problem in reading bam files with EDASeq   Raffaele A Calogero
• [BioC] LVSmiRNA for EList,   Stefano Calza
• [BioC] GB_ACC to Entrez ids   Vincent Carey
• [BioC] genotyping output files   Vincent Carey
• [BioC] ggbio and R-2.14.0   Vincent Carey
• [BioC] GenomicRanges functions unlist(GRangesList(x)) throw an error when used from an installed package   Vincent Carey
• [BioC] Saureus.db Files   Vincent Carey
• [BioC] Difference between go, with_go and with_go_go   Marc Carlson
• [BioC] Saureus Affy Chip   Marc Carlson
• [BioC] limma topTable with gene symbols in output: annotate problem   Carlson, Marc R
• [BioC] KEGGSOAP   Carlson, Marc R
• [BioC] A bug in either KEGG or KEGGSOAP?   Carlson, Marc R
• [BioC] RMA normalisation of test microarray data to training data   Benilton Carvalho
• [BioC] genotyping output files   Benilton Carvalho
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Benilton Carvalho
• [BioC] package charm, creating .xys files   Benilton Carvalho
• [BioC] package charm, creating .xys files   Benilton Carvalho
• [BioC] how edgeR control the outliers?   Robert Castelo
• [BioC] Hu Gene 1.0 ST v1 microarray processing and analysis   Azby Cdex
• [BioC] A bug in either KEGG or KEGGSOAP?   Sang Chul Choi
• [BioC] GenomicRanges functions unlist(GRangesList(x)) throw an error when used from an installed package   Simon Coetzee
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Malcolm Cook
• [BioC] Access to archived versions of Ensembl with biomaRt   Cook, Malcolm
• [BioC] rtracklayer laying a track   Cook, Malcolm
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Cook, Malcolm
• [BioC] GRanges setdiff With Features on Both Strands   Cook, Malcolm
• [BioC] GRanges setdiff With Features on Both Strands   Cook, Malcolm
• [BioC] Access to archived versions of Ensembl with biomaRt   Adrián Cortés
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Sean Davis
• [BioC] mapping protein domains to exons   Sean Davis
• [BioC] how to set R memory limit   Sean Davis
• [BioC] how to set R memory limit   Sean Davis
• [BioC] how to set R memory limit   Sean Davis
• [BioC] Summarizing two-channel data (RGList, MAList) for limma analysis   Sean Davis
• [BioC] how to solve the memory problem   Sean Davis
• [BioC] [Rocky] - LIMMA to identify deferentially expressed genes   Sean Davis
• [BioC] how to replace NA by 1   Sean Davis
• [BioC] Strecth of N's in between reads   Sean Davis
• [BioC] Mailing list   Sean Davis
• [BioC] ChIP-seq peaks in the vicinity of refseq exons   Sean Davis
• [BioC] PFAM gene enrichment test using GOstats and Category   Davis, Wade
• [BioC] Heatmap.2 Trace Line Thickness   Davis, Wade
• [BioC] HTqPCR and Biobase's eSet   De Bondt, An-7114 [JRDBE]
• [BioC] A bug in either KEGG or KEGGSOAP?   Diego Diez
• [BioC] htSeqTools - naming RangedData objects?   Ian Donaldson
• [BioC] htSeqTools - filtered reads > BED?   Ian Donaldson
• [BioC] DESeq - ChIP-seq (including background reads)   Ian Donaldson
• [BioC] rGADEM crash   Arnaud Droit
• [BioC] Fwd: differential binding question   Heidi Dvinge
• [BioC] HTqPCR problem with replicates   Heidi Dvinge
• [BioC] HTqPCR and Biobase's eSet   Heidi Dvinge
• [BioC] processSwathData for HumanHT-12 v4   Stephen Edwards
• [BioC] HTqPCR problem with replicates   Marco Fabbri
• [BioC] Rgraphviz installing problem   Alexandra Federer
• [BioC] limma: adding weights to mroast   Anthoula Gaigneaux
• [BioC] edgeR -- gene expression variability   Miguel Gallach
• [BioC] edgeR -- gene expression variability   Miguel Gallach
• [BioC] edgeR -- gene expression variability   Miguel Gallach
• [BioC] DESeq estimateDispersion query   Iain Gallagher
• [BioC] Error message when trying to create enrichment maps in HTSanalyzeR   Catherine Garry
• [BioC] limma design matrix   Walter Glaser
• [BioC] ilumina CanineHD   Vidhya Gnanasekaran
• [BioC] Heatmap.2 Trace Line Thickness   Michael Goodson
• [BioC] how to get a list of the genes in each module in WGCNA   Christopher T Gregg
• [BioC] OpenSuse 11.4, cannot install Bioconductor due to missing C compiler   Ivan Gregoretti
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Groot, Philip de
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Groot, Philip de
• [BioC] BaseCounts & edgeR   Marco Groth
• [BioC] Problem with limma's topTable lfc filter when more than 1 contrast is in output   Alex Gutteridge
• [BioC] I AM NEW USER TO XCMS AND REALLY NEED HELP!   HABIBALLAH HAMZEHZARGHANI
• [BioC] Summarizing two-channel data (RGList, MAList) for limma analysis   Daniel Aaen Hansen
• [BioC] down-weighting control probes in limma (with Agilent arrays)?   Daniel Aaen Hansen
• [BioC] Bioconductor Digest, Vol 107, Issue 1   Peter Haverty
• [BioC] About Multicore: mclapply   Prashantha Hebbar
• [BioC] Is there any way to merge all yeilds of FastqStreamer?   Prashantha Hebbar
• [BioC] edgeR package : question about 'exactTest' results   NEIL-BERNET Helen
• [BioC] edgeR package : question about 'exactTest' results   NEIL-BERNET Helen
• [BioC] edgeR package : question about 'exactTest' results   NEIL-BERNET Helen
• [BioC] question subsetting expressionSet   Hooiveld, Guido
• [BioC] GB_ACC to ENTREZ_ID   Hans-Rudolf Hotz
• [BioC] biomart to a data.frame   Hans-Rudolf Hotz
• [BioC] Genotype calls for Illumina Omni5   Hu, Donglei
• [BioC] edgeR dataset filtering using pnas_expression.txt   Wolfgang Huber
• [BioC] DESeq for an mRNA-seq time course   Wolfgang Huber
• [BioC] Summarizing two-channel data (RGList, MAList) for limma analysis   Wolfgang Huber
• [BioC] DESeq mean,var   Wolfgang Huber
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Wolfgang Huber
• [BioC] visualization of chromosome interactions   Wolfgang Huber
• [BioC] refseq to genesymbol with BiomaRt - problem occurs   Wolfgang Huber
• [BioC] shift function (GenomicRanges, IRanges), issue with negative start values and circular DNA   Ivanek, Robert
• [BioC] a question about trimLRPatterns?   Harris A. Jaffee
• [BioC] a question about trimLRPatterns?   Harris A. Jaffee
• [BioC] is matchPattern faster?   Harris A. Jaffee
• [BioC] is matchPattern faster?   Harris A. Jaffee
• [BioC] is matchPattern faster?   Harris A. Jaffee
• [BioC] intern=TRUE seems not working in system command in Mac OS   Harris A. Jaffee
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Bas Jansen
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Bas Jansen
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Bas Jansen
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Bas Jansen
• [BioC] edgeR--CalcNormFactors   chris Jhon
• [BioC] down-weighting control probes in limma (with Agilent arrays)?   Maciej Jończyk
• [BioC] open positions in Bioinformatics Department at Genentech   Josh Kaminker
• [BioC] Postdoctoral position at Novartis, Basel   Kauffmann, Audrey
• [BioC] Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!   Moritz Kebschull
• [BioC] Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!   Moritz Kebschull
• [BioC] Contrasts for 3x2 factorial experiment in R/edgeR   Benjamin King
• [BioC] Caught segfault when running MEDIPS package   Asta Laiho
• [BioC] Continuation of the KEGG.db package   Asta Laiho
• [BioC] I want to unsuscribe from The Bioconductor Project Mailing List   Maximiliano Sánchez Lamas
• [BioC] OpenSuse 11.4, cannot install Bioconductor due to missing C compiler   Lapointe, David
• [BioC] rtracklayer laying a track   Michael Lawrence
• [BioC] rtracklayer laying a track   Michael Lawrence
• [BioC] rtracklayer laying a track   Michael Lawrence
• [BioC] rtracklayer laying a track   Michael Lawrence
• [BioC] about reduce function in GenomicRanges   Michael Lawrence
• [BioC] about reduce function in GenomicRanges   Michael Lawrence
• [BioC] GRanges setdiff With Features on Both Strands   Michael Lawrence
• [BioC] htSeqTools - naming RangedData objects?   Michael Lawrence
• [BioC] about reduce function in GenomicRanges   Michael Lawrence
• [BioC] GRanges setdiff With Features on Both Strands   Michael Lawrence
• [BioC] GRanges setdiff With Features on Both Strands   Michael Lawrence
• [BioC] rtrackplayer UCSC multiz maf download   Michael Lawrence
• [BioC] Importing error using rtracklayer's "import" function   Michael Lawrence
• [BioC] Importing error using rtracklayer's "import" function   Michael Lawrence
• [BioC] htSeqTools - filtered reads > BED?   Michael Lawrence
• [BioC] rtracklayer error   Michael Lawrence
• [BioC] using ensembl archive in GenomicRanges   Paul Leo
• [BioC] Rsamtools BAM File Opening Takes Long Time   Paul Leo
• [BioC] Basic question about GENE 1.0 ST   Guido Leoni
• [BioC] problem with preprocessCore   Guido Leoni
• [BioC] rtracklayer error   Lescai, Francesco
• [BioC] VariantAnnotation updated - error in predictCoding   Lescai, Francesco
• [BioC] package charm, creating .xys files   Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare
• [BioC] package charm, creating .xys files   Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare
• [BioC] package charm, creating .xys files   Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare
• [BioC] package charm, creating .xys files   Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare
• [BioC] installation of Rsamtools   Steve Lianoglou
• [BioC] Fwd: differential binding question   Steve Lianoglou
• [BioC] Genomic Ranges. Ignore strandedness in findOverlap function.   Steve Lianoglou
• [BioC] how to set R memory limit   Steve Lianoglou
• [BioC] how to set R memory limit   Steve Lianoglou
• [BioC] CummeRbund Error   Steve Lianoglou
• [BioC] rho statistics for dinucleotide abundance from a sequence file   Steve Lianoglou
• [BioC] about reduce function in GenomicRanges   Steve Lianoglou
• [BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13   Steve Lianoglou
• [BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13   Steve Lianoglou
• [BioC] GRanges setdiff With Features on Both Strands   Steve Lianoglou
• [BioC] biomart to a data.frame   Steve Lianoglou
• [BioC] probability of a point membership to a certain cluster   Steve Lianoglou
• [BioC] probability of a point membership to a certain cluster   Steve Lianoglou
• [BioC] I want to unsuscribe from The Bioconductor Project Mailing List   Steve Lianoglou
• [BioC] PFAM gene enrichment test using GOstats and Category   Henrik Hjarvard de Fine Licht
• [BioC] how to set R memory limit   Sunny Yu Liu
• [BioC] How to make a custom cdf file?   Olivier Lucas
• [BioC] Strecth of N's in between reads   MLSC MANIPAL
• [BioC] limma design matrix   MacDonald, James
• [BioC] Hu Gene 1.0 ST v1 microarray processing and analysis   James W. MacDonald
• [BioC] RMA normalisation of test microarray data to training data   James W. MacDonald
• [BioC] How remove controls probes - Affymetrix Gene   James W. MacDonald
• [BioC] how limma compute the logFC in differential expression analysis   James W. MacDonald
• [BioC] Annotating limma results: Affymetrix probe IDs not mapping to hugene10stprobeset.db   James W. MacDonald
• [BioC] using limma package for paired t-test: Error: (subscript) logical subscript too long   James W. MacDonald
• [BioC] I AM NEW USER TO XCMS AND REALLY NEED HELP!   James W. MacDonald
• [BioC] using limma package for paired t-test: Error: (subscript) logical subscript too long   James W. MacDonald
• [BioC] miRNA normalisation   James W. MacDonald
• [BioC] miRNA normalisation   James W. MacDonald
• [BioC] 2 color microarray and decidetests output   James W. MacDonald
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   James W. MacDonald
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   James W. MacDonald
• [BioC] help with limma design,contrast matrix please   James W. MacDonald
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   James W. MacDonald
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   James W. MacDonald
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   James W. MacDonald
• [BioC] Two populations on microarray   Joaquin Martinez
• [BioC] Genomic Ranges. Ignore strandedness in findOverlap function.   Fahim Mohammad
• [BioC] Genomic Ranges. Ignore strandedness in findOverlap function.   Fahim Mohammad
• [BioC] [RESOLVED] Genomic Ranges. Ignore strandedness in findOverlap function.   Fahim Mohammad
• [BioC] LVSmiRNA for EList,   Ali Mohammadian
• [BioC] DESeq mean,var   Bruce Moran(External)
• [BioC] KEGGsoap: Space required after the Public Identifier   Martin Morgan
• [BioC] problem with preprocessCore   Martin Morgan
• [BioC] scanBamHeader for File on Internet   Martin Morgan
• [BioC] question subsetting expressionSet   Martin Morgan
• [BioC] about the quality score   Martin Morgan
• [BioC] about the quality score   Martin Morgan
• [BioC] questions on cghMCR package   Martin Morgan
• [BioC] [R-sig-hpc] About Multicore: mclapply   Martin Morgan
• [BioC] ggbio and R-2.14.0   Martin Morgan
• [BioC] ChiPpeakAnno: findOverlappingPeaks: running time   Martin Morgan
• [BioC] ggbio and R-2.14.0   Martin Morgan
• [BioC] Rsamtools BAM File Opening Takes Long Time   Martin Morgan
• [BioC] using limma package for paired t-test: Error: (subscript) logical subscript too long   Martin Morgan
• [BioC] narrow on GappedAlignments fails with error   Martin Morgan
• [BioC] Workshop, Feb 27/28: Advanced R / Bioconductor Workshop on High-Throughput Genetic Analysis   Martin Morgan
• [BioC] Is there any way to merge all yeilds of FastqStreamer?   Martin Morgan
• [BioC] Rgraphviz installing problem   Martin Morgan
• [BioC] biomart to a data.frame   Martin Morgan
• [BioC] URGENT Help required: Getting this error with GAGE analysis   Martin Morgan
• [BioC] CNTools error message   Martin Morgan
• [BioC] Rgraphviz: fail to plot   Martin Morgan
• [BioC] FW: URGENT Help required: Getting this error with GAGE analysis, input files attached   Martin Morgan
• [BioC] Error with GAGE   Martin Morgan
• [BioC] miRNA normalisation   Dermot Morris
• [BioC] miRNA normalisation   Dermot Morris
• [BioC] Importing error using rtracklayer's "import" function   Kavitha Mukund
• [BioC] Importing error using rtracklayer's "import" function   Kavitha Mukund
• [BioC] ChIP-seq peaks in the vicinity of refseq exons   Kavitha Mukund
• [BioC] MEDIPS R package reference genomes   Valerie Obenchain
• [BioC] CummeRbund Error   Valerie Obenchain
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Valerie Obenchain
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Valerie Obenchain
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Valerie Obenchain
• [BioC] problem in reading bam files with EDASeq   Valerie Obenchain
• [BioC] Error message when trying to create enrichment maps in HTSanalyzeR   Valerie Obenchain
• [BioC] writing BAM files from within R   Valerie Obenchain
• [BioC] Help With RNA-seq   Valerie Obenchain
• [BioC] [Rocky] - R code for PGSEA package to identify differentially expressed genes   Valerie Obenchain
• [BioC] [Rocky] - R code for PGSEA package to identify differentially expressed genes   Valerie Obenchain
• [BioC] Help With RNA-seq   Valerie Obenchain
• [BioC] VariantAnnotation updated - error in predictCoding   Valerie Obenchain
• [BioC] VariantAnnotation updated - error in predictCoding   Valerie Obenchain
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Osselaer, Steven [JRDBE Extern]
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Osselaer, Steven [JRDBE Extern]
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Osselaer, Steven [JRDBE Extern]
• [BioC] Problems normalizing scanarray express data with limma   Matthew Ouellette
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Hervé Pagès
• [BioC] pairwise alignment and homology score   Hervé Pagès
• [BioC] pairwise alignment and homology score   Hervé Pagès
• [BioC] shift function (GenomicRanges, IRanges), issue with negative start values and circular DNA   Hervé Pagès
• [BioC] GRanges setdiff With Features on Both Strands   Hervé Pagès
• [BioC] shift function (GenomicRanges, IRanges), issue with negative start values and circular DNA   Hervé Pagès
• [BioC] GRanges setdiff With Features on Both Strands   Hervé Pagès
• [BioC] GRanges setdiff With Features on Both Strands   Hervé Pagès
• [BioC] Saureus Affy Chip   Marcos Pinho
• [BioC] Saureus.db Files   Marcos Pinho
• [BioC] create GeneSetCollection from OBOCollection   Wendy Qiao
• [BioC] GenomicFeatures makeTranscriptDbFromBiomart failure   Tim Rayner
• [BioC] narrow on GappedAlignments fails with error   Hubert Rehrauer
• [BioC] htSeqTools: using GRanges and GRangesList   Oscar Reina
• [BioC] ilumina CanineHD   Matthew Ritchie
• [BioC] normalizing time course RNA-Seq data   Mark Robinson
• [BioC] differential binding question   Mark Robinson
• [BioC] normalization factors for ChIP/RNA-IP-seq data   Mark Robinson
• [BioC] edgeR--CalcNormFactors   Mark Robinson
• [BioC] edgeR package : question about 'exactTest' results   Mark Robinson
• [BioC] htSeqTools - naming RangedData objects?   David Rossell
• [BioC] Basic question about GENE 1.0 ST   David Ruau
• [BioC] Rgraphviz: fail to plot   Håvard Rue
• [BioC] Caught segfault when running MEDIPS package   Oscar Rueda
• [BioC] Advanced RNA-Seq and ChiP-Seq Data Analysis course, 1-4 May 2012   Gabriella Rustici
• [BioC] Advanced RNA-Seq and ChiP-Seq Data Analysis course, 1-4 May 2012   Gabriella Rustici
• [BioC] genotyping output files   Rafiq S.
• [BioC] genotyping output files   Rafiq S.
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Javerjung Sandhu
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Javerjung Sandhu
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Javerjung Sandhu
• [BioC] FW: URGENT Help required: Getting this error with GAGE analysis, input files attached   Javerjung Sandhu
• [BioC] rtracklayer laying a track   Simon Schaffrr
• [BioC] Mailing list   Shen, Xiangling
• [BioC] KEGGSOAP   Ricardo Silva
• [BioC] GB_ACC to Entrez ids   Reema Singh
• [BioC] GB_ACC to ENTREZ_ID   Reema Singh
• [BioC] processSwathData for HumanHT-12 v4   Mike Smith
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Mike Smith
• [BioC] limma: adding weights to mroast   Gordon K Smyth
• [BioC] limma - 2-color agilent microarray, GO annotation   Gordon K Smyth
• [BioC] Contrasts for 3x2 factorial experiment in R/edgeR   Gordon K Smyth
• [BioC] Contrasts for 3x2 factorial experiment in R/edgeR   Gordon K Smyth
• [BioC] edgeR -- gene expression variability   Gordon K Smyth
• [BioC] edgeR -- gene expression variability   Gordon K Smyth
• [BioC] Why edgeR ouput some p values larger than 1   Gordon K Smyth
• [BioC] Why edgeR ouput some p values larger than 1   Gordon K Smyth
• [BioC] limma: adding weights to mroast   Gordon K Smyth
• [BioC] Problems normalizing scanarray express data with limma   Gordon K Smyth
• [BioC] Problems normalizing scanarray express data with limma   Gordon K Smyth
• [BioC] Two populations on microarray   Gordon K Smyth
• [BioC] Two populations on microarray   Gordon K Smyth
• [BioC] Problem with limma's topTable lfc filter when more than 1 contrast is output   Gordon K Smyth
• [BioC] mergeScans functions in limma - minFactor error   Gordon K Smyth
• [BioC] how edgeR control the outliers?   Gordon K Smyth
• [BioC] Please help! How to specify factors for a RCBD in edgeR   Gordon K Smyth
• [BioC] DESeq for an mRNA-seq time course   Elena Sorokin
• [BioC] DESeq for an mRNA-seq time course   Elena Sorokin
• [BioC] 2 color microarray decidetests Output   Srinivas Srikanth
• [BioC] 2 color microarray and decidetests output   Srinivas M. Srikanth
• [BioC] Fwd: differential binding question   Rory Stark
• [BioC] Fwd: differential binding question   Rory Stark
• [BioC] differential binding question   Rory Stark
• [BioC] edgeR package : question about 'exactTest' results   Rory Stark
• [BioC] edgeR package : question about 'exactTest' results   Rory Stark
• [BioC] scanBamHeader for File on Internet   Dario Strbenac
• [BioC] scanBamHeader for File on Internet   Dario Strbenac
• [BioC] GRanges setdiff With Features on Both Strands   Dario Strbenac
• [BioC] Rsamtools BAM File Opening Takes Long Time   Dario Strbenac
• [BioC] GRanges setdiff With Features on Both Strands   Dario Strbenac
• [BioC] visualization of chromosome interactions   Bogdan Tanasa
• [BioC] edgeR dataset filtering using pnas_expression.txt   Dave Tang
• [BioC] Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!   Tarca, Adi
• [BioC] about reduce function in GenomicRanges   Tarca, Adi
• [BioC] about reduce function in GenomicRanges   Tarca, Adi
• [BioC] about reduce function in GenomicRanges   Tarca, Adi
• [BioC] about reduce function in GenomicRanges   Tarca, Adi
• [BioC] Bioconductor AMI NOT FOUND   Dan Tenenbaum
• [BioC] Bioconductor AMI NOT FOUND   Dan Tenenbaum
• [BioC] Bioconductor AMI NOT FOUND   Dan Tenenbaum
• [BioC] OpenSuse 11.4, cannot install Bioconductor due to missing C compiler   Dan Tenenbaum
• [BioC] problem in reading bam files with EDASeq   Dan Tenenbaum
• [BioC] tcltk package for R 2.14.1   Dan Tenenbaum
• [BioC] tcltk package for R 2.14.1   Dan Tenenbaum
• [BioC] Installing bioconductor with openSUSE 11.4 and R 2.14   Dan Tenenbaum
• [BioC] Rgraphviz: fail to plot   Dan Tenenbaum
• [BioC] Rgraphviz: fail to plot   Dan Tenenbaum
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Sebastian Thieme
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   Sebastian Thieme
• [BioC] how to set R memory limit   Sebastian Thieme
• [BioC] biomart to a data.frame   Sebastian Thieme
• [BioC] Removing continuous confounding technical variables by using ComBat in SVA package or another approach   Djie Tjwan Thung
• [BioC] Adjusting removeBatchEffect from limma   Djie Tjwan Thung
• [BioC] Why edgeR ouput some p values larger than 1   Yuan Tian
• [BioC] how limma compute the logFC in differential expression analysis   Yuan Tian
• [BioC] DESeq: how to get the variance information   Yuan Tian
• [BioC] how edgeR control the outliers?   Yuan Tian
• [BioC] HTqPCR useful for ChIP data ?   Guillaume Tiberi
• [BioC] Continuation of the KEGG.db package   Tim Triche, Jr.
• [BioC] [lumi] methyLumiR upload error of 450k   Tim Triche, Jr.
• [BioC] Two populations on microarray   Ben Tupper
• [BioC] Summarizing two-channel data (RGList, MAList) for limma analysis   Stephen Turner
• [BioC] limma topTable with gene symbols in output: annotate problem   Stephen Turner
• [BioC] Annotating limma results: Affymetrix probe IDs not mapping to hugene10stprobeset.db   Stephen Turner
• [BioC] probability of a point membership to a certain cluster   Barbara Uszczynska
• [BioC] probability of a point membership to a certain cluster   Barbara Uszczynska
• [BioC] probability of a point membership to a certain cluster   Barbara Uszczynska
• [BioC] MEDIPS R package reference genomes   Vining, Kelly
• [BioC] MLInterfaces, CMA, or Caret for censored survival?   Levi Waldron
• [BioC] mapping snp array probe to a gene, biomaRt or others?   Xiaokuan Wei
• [BioC] GAGE vs other GO analysis tools   Luo Weijun
• [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files   Luo Weijun
• [BioC] Error with GAGE   Luo Weijun
• [BioC] Continuation of the KEGG.db package   January Weiner
• [BioC] GAGE vs other GO analysis tools   January Weiner
• [BioC] Comparing single and two-color arrays   January Weiner
• [BioC] ggbio and R-2.14.0   Weiner, Michael
• [BioC] ggbio and R-2.14.0   Weiner, Michael
• [BioC] ggbio and R-2.14.0   Weiner, Michael
• [BioC] [lumi] methyLumiR upload error of 450k   Geoff Woodward
• [BioC] [lumi] methyLumiR upload error of 450k   Geoff Woodward
• [BioC] [lumi] 450k methylation color correction issue.   Geoff Woodward
• [BioC] Summarizing two-channel data (RGList, MAList) for limma analysis   Samuel Wuest
• [BioC] tcltk package for R 2.14.1   Chintan Vora - Xcelris
• [BioC] tcltk package for R 2.14.1   Chintan Vora - Xcelris
• [BioC] tcltk package for R 2.14.1   Chintan Vora - Xcelris
• [BioC] limma design matrix   Assa Yeroslaviz
• [BioC] limma design matrix   Assa Yeroslaviz
• [BioC] plot with two x-axis   Assa Yeroslaviz
• [BioC] biomart to a data.frame   Assa Yeroslaviz
• [BioC] biomart to a data.frame   Assa Yeroslaviz
• [BioC] visualization of chromosome interactions   Tengfei Yin
• [BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13   Peng Yu
• [BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13   Peng Yu
• [BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13   Peng Yu
• [BioC] About BioMart   Zhi Zhang
• [BioC] ChiPpeakAnno: findOverlappingPeaks: running time   Zhu, Lihua (Julie)
• [BioC] ChiPpeakAnno: findOverlappingPeaks: running time   Zhu, Lihua (Julie)
• [BioC] Problem with limma's topTable lfc filter when more than 1 contrast is in output   Vladimir Zhurov
• [BioC] Problem with limma's topTable lfc filter when more than 1 contrast is in output   Vladimir Zhurov
• [BioC] Problem with limma's topTable lfc filter when more than 1 contrast is output   Vladimir Zhurov
• [BioC] Caught segfault when running MEDIPS package   Asta Laiho [guest]
• [BioC] how to get a list of the genes in each module in WGCNA   Christopher Gregg [guest]
• [BioC] rtrackplayer UCSC multiz maf download   Evan [guest]
• [BioC] CardioNet PhD Student in Madrid, Spain   Fatima Sanchez-Cabo [guest]
• [BioC] ChiPpeakAnno: findOverlappingPeaks: running time   George [guest]
• [BioC] Rgraphviz: fail to plot   HÃ¥vard Rue [guest]
• [BioC] URGENT Help required: Getting this error with GAGE analysis   Jung [guest]
• [BioC] Affymetrix Gene array probe coordinates, mogene10stv1probe   Leo Schalkwyk [guest]
• [BioC] How remove controls probes - Affymetrix Gene   Sophie Lamarre [guest]
• [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips   Steven Osselaer [guest]
• [BioC] rho statistics for dinucleotide abundance from a sequence file   Utpal Bakshi [guest]
• [BioC] Bioconductor AMI NOT FOUND   glynn [guest]
• [BioC] rtracklayer laying a track   simon [guest]
• [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....   axel.klenk at actelion.com
• [BioC] Caught segfault when running MEDIPS package   chavez
• [BioC] [XPS] Background computation on single CEL file   cstrato
• [BioC] error in compute contrasts for two color data   sara domingos
• [BioC] [Rocky] - R code for PGSEA package to identify differentially expressed genes   haojam
• [BioC] CummeRbund Error   john herbert
• [BioC] CummeRbund Error   john herbert
• [BioC] CummeRbund Error   john herbert
• [BioC] miRNA array normalization - RMA vs Genespring comparison   andrea.grilli at ior.it
• [BioC] refseq to genesymbol with BiomaRt - problem occurs   andrea.grilli at ior.it
• [BioC] Limma design for paired t-test for multiple subgroups   viritha k
• [BioC] using limma package for paired t-test: Error: (subscript) logical subscript too long   viritha k
• [BioC] using limma package for paired t-test: Error: (subscript) logical subscript too long   viritha k
• [BioC] question subsetting expressionSet   J.Oosting at lumc.nl
• [BioC] genotyping output files   J.Oosting at lumc.nl
• [BioC] Access to archived versions of Ensembl with biomaRt   mjonczyk
• [BioC] writing BAM files from within R   margherita mutarelli
• [BioC] questions on cghMCR package   nathalie
• [BioC] Package tO identify minimum common genomic region from CGH data   nathalie
• [BioC] CNTools error message   nathalie
• [BioC] how to set R memory limit   wang peter
• [BioC] about the quality score   wang peter
• [BioC] about the quality score   wang peter
• [BioC] about the quality score   wang peter
• [BioC] how to solve the memory problem   wang peter
• [BioC] a question about trimLRPatterns?   wang peter
• [BioC] is matchPattern faster?   wang peter
• [BioC] how to replace NA by 1   wang peter
• [BioC] problem in reading bam files with EDASeq   rcaloger
• [BioC] intern=TRUE seems not working in system command in Mac OS   rcaloger
• [BioC] KEGGsoap: Space required after the Public Identifier   seth redmond
• [BioC] problem in reading bam files with EDASeq   davide risso
• [BioC] probe exclusion in Affy - problem with Removeprobes function   mahulchakraborty at rochester.edu
• [BioC] Fwd: differential binding question   mali salmon
• [BioC] Fwd: differential binding question   mali salmon
• [BioC] differential binding question   mali salmon
• [BioC] normalization factors for ChIP/RNA-IP-seq data   mali salmon
• [BioC] normalization factors for ChIP/RNA-IP-seq data   mali salmon
• [BioC] [XPS] Background computation on single CEL file   thomas sierocinski
• [BioC] mapping protein domains to exons   anupam sinha
• [BioC] using ensembl archive in GenomicRanges   anupam sinha
• [BioC] pairwise alignment and homology score   erikafalisi at tin.it
• [BioC] [lumi] methyLumiR upload error of 450k   wei wang
• [BioC] a question about how to use ChIPseqR   humburg at well.ox.ac.uk
• [BioC] mergeScans function in limma - minFactor error   Agnieszka Żmieńko
• [BioC] [Rocky] - LIMMA to identify deferentially expressed genes   하오잠 로

Last message date: Tue Jan 31 22:16:43 CET 2012
Archived on: Thu Feb 2 18:54:21 CET 2012

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