May 2012 Archives by author

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Starting: Tue May 1 02:27:04 CEST 2012
Ending: Thu May 31 23:53:42 CEST 2012
Messages: 599

• [BioC] Problem creating expression set.   dha 2001
• [BioC] Problem creating expression set.   dha 2001
• [BioC] Random Forest Code   Bahar AZ
• [BioC] How to open the edgeR Users Guide within R?   Cei Abreu-Goodger
• [BioC] Top 10% of genes based on p-value in TopTable   Ovokeraye Achinike-Oduaran
• [BioC] Top 10% of genes based on p-value in TopTable   Ovokeraye Achinike-Oduaran
• [BioC] Top 10% of genes based on p-value in TopTable   Ovokeraye Achinike-Oduaran
• [BioC] Limma: Top 10% gene list based on p-values   Ovokeraye Achinike-Oduaran
• [BioC] Limma: Top 10% gene list based on p-values   Ovokeraye Achinike-Oduaran
• [BioC] ReadAffy() Error - 2 Platforms in one file   Ovokeraye Achinike-Oduaran
• [BioC] ReadAffy() Error - 2 Platforms in one file   Ovokeraye Achinike-Oduaran
• [BioC] ReadAffy() Error - 2 Platforms in one file   Ovokeraye Achinike-Oduaran
• [BioC] Extracting topTable data from saved file   Ovokeraye Achinike-Oduaran
• [BioC] Extracting topTable data from saved file   Ovokeraye Achinike-Oduaran
• [BioC] Extracting topTable data from saved file   Ovokeraye Achinike-Oduaran
• [BioC] PANTHER in R.... Gene lists in sigPathway?   Ovokeraye Achinike-Oduaran
• [BioC] PANTHER in R.... Gene lists in sigPathway?   Ovokeraye Achinike-Oduaran
• [BioC] PANTHER in R.... Gene lists in sigPathway?   Ovokeraye Achinike-Oduaran
• [BioC] Genes to SNPs Tool   Ovokeraye Achinike-Oduaran
• [BioC] KEGG pathway heat map   Felipe Antonio Riveroll Aguirre
• [BioC] KEGG pathway heat map   Felipe Riveroll Aguirre
• [BioC] PANTHER in R.... Gene lists in sigPathway?   Felipe Riveroll Aguirre
• [BioC] PANTHER in R.... Gene lists in sigPathway?   Felipe Riveroll Aguirre
• [BioC] help with mapping statistics summary   Kemal Akman
• [BioC] easyRNAseq question   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] easyRNAseq question   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] edgeR outlier question   Guffanti Alessandro
• [BioC] miRNA and other small RNAs   Guffanti Alessandro
• [BioC] non-integer counts for edgeR   Guffanti Alessandro
• [BioC] Limma analyses;paired and/or factorial design?   Naomi Altman
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Simon Anders
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Simon Anders
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Simon Anders
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Simon Anders
• [BioC] How to use DESeq output to convert raw counts to normalized data   Simon Anders
• [BioC] DESeq error with glm.fit during estimateDispersions   Simon Anders
• [BioC] DESeq error thrown during estimateDispersions w/ coxReid method   Simon Anders
• [BioC] easyRNAseq question   Simon Anders
• [BioC] DEXSeq filtering   Simon Anders
• [BioC] R IDE editor   Robert Baer
• [BioC] 450K annotation: discrepancy between GEO GPL and Bioconductor annotation   Bartlett, Thomas
• [BioC] GEOquery install problem with openSUSE 11.4 and R 2.15   Bartlett, Thomas
• [BioC] xvalSpec('NOTEST') problem   Gustavo Fernández Bayón
• [BioC] Package for doing Copy number analsysi with LOH   Henrik Bengtsson
• [BioC] Problem with "ragene10stprobeset.db" package   Laura Bermúdez
• [BioC] Convert gene symbols to ensembl id   Fred Boehm
• [BioC] R IDE editor   Aaron Brandes
• [BioC] xvalSpec('NOTEST') problem   Vincent Carey
• [BioC] xvalSpec('NOTEST') problem   Vincent Carey
• [BioC] 'citation("RBGL")' command produces package not found error   Vincent Carey
• [BioC] 'citation("RBGL")' command produces package not found error   Vincent Carey
• [BioC] GOSim yeast   Marc Carlson
• [BioC] Error loading charm   Benilton Carvalho
• [BioC] Error loading charm   Benilton Carvalho
• [BioC] Error loading charm   Benilton Carvalho
• [BioC] pdInfoBuilder: coreMps   Benilton Carvalho
• [BioC] Using BrainArray mappings with oligo package   Benilton Carvalho
• [BioC] help with mapping statistics summary   Leonor Carvalho
• [BioC] edgeR outlier question   Robert Castelo
• [BioC] Moderated t-test   Chintanu
• [BioC] Moderated t-test   Chintanu
• [BioC] Moderated t-test   Chintanu
• [BioC] Moderated t-test   Chintanu
• [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?   Sang Chul Choi
• [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?   Sang Chul Choi
• [BioC] non-integer counts for edgeR   Mete Civelek
• [BioC] Copy Number Analysis across multiple SNP array plaforms   Djork-Arné Clevert
• [BioC] R IDE editor   Djork-Arné Clevert
• [BioC] outlier probes detection   Djork-Arné Clevert
• [BioC] outlier probes detection   Djork-Arné Clevert
• [BioC] eset -Affy Mouse Gene 1.0 ST. Array-   Djork-Arné Clevert
• [BioC] Newbie. quantile normalization should be done on all conditions or within replicates of each condition?   Cytochalasin
• [BioC] How do I find up and down regulated genes for each contrast in LIMMA?   Sean Davis
• [BioC] Adding a column to phenoData dataframe   Sean Davis
• [BioC] FDR calculation for expression array   Sean Davis
• [BioC] Limma: Top 10% gene list based on p-values   Sean Davis
• [BioC] ReadAffy() Error - 2 Platforms in one file   Sean Davis
• [BioC] ReadAffy() Error - 2 Platforms in one file   Sean Davis
• [BioC] GSEA with methylation data   Sean Davis
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   Sean Davis
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   Sean Davis
• [BioC] GEOquery install problem with openSUSE 11.4 and R 2.15   Sean Davis
• [BioC] useDevel() not working   Sean Davis
• [BioC] useDevel() not working   Sean Davis
• [BioC] Amplicon and exon level read counts and GC content   Sean Davis
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   Sean Davis
• [BioC] MacOS Package installation problems   Sean Davis
• [BioC] Rsubread package usage and speed questions   Davis, Wade
• [BioC] Rsubread package usage and speed questions   Davis, Wade
• [BioC] DESeq Package Questions   Xin Davis
• [BioC] How to use DESeq output to convert raw counts to normalized data   Xin Davis
• [BioC] FastqStreamer   Marcus Davy
• [BioC] FastqStreamer   Marcus Davy
• [BioC] build/check reports for ENVISIONQuery, IdMappingRetrieval on OSX   Day, Roger S
• [BioC] Fwd: [Bioc-devel] Changes in the %in% function for DNAStringSet?   Nicolas Delhomme
• [BioC] easyRNASeq Error in counting from C.elegans   Nicolas Delhomme
• [BioC] easyRNAseq question   Nicolas Delhomme
• [BioC] easyRNAseq question   Nicolas Delhomme
• [BioC] Top 10% of genes based on p-value in TopTable   Dan Du
• [BioC] FDR calculation for expression array   Dan Du
• [BioC] Human Illumina Methylation27k question   Pan Du
• [BioC] question with reading bead summary data into beadarray   Mark Dunning
• [BioC] HTqPCR   Heidi Dvinge
• [BioC] HTqPCR   Heidi Dvinge
• [BioC] stable gene in microarray   Marco Fabbri
• [BioC] subreddit for R related stuff   Robert M. Flight
• [BioC] fitting growth curve   Andreia Fonseca
• [BioC] fitting growth curve   Andreia Fonseca
• [BioC] fitting growth curve   Andreia Fonseca
• [BioC] Rsamtools: scanBamFlag bug?   Nuno Fonseca
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Richard Friedman
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Richard Friedman
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Richard Friedman
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Richard Friedman
• [BioC] Building specific Ortoghonal contrasts in LIMMA   Garcia Orellana,Miriam
• [BioC] Building specific Ortoghonal contrasts in LIMMA   Garcia Orellana,Miriam
• [BioC] Finding coding SNPs with predictCoding   Thomas Girke
• [BioC] Limma, design matrix, lmfit Coefficients not estimable error   Varshna Goelela
• [BioC] Package for doing Copy number analsysi with LOH   Stephanie M. Gogarten
• [BioC] Excessive memory requirements of PING or bug?   Raphael Gottardo
• [BioC] gene set enrichment analysis of RNA-Seq data   Paolo Guarnieri
• [BioC] Odd behaviour with renameSeqlevels   Alex Gutteridge
• [BioC] Odd behaviour with renameSeqlevels   Alex Gutteridge
• [BioC] LIMMA decideTests result zero from contrast matrix   Alex Gutteridge
• [BioC] v is for values()   Kasper Daniel Hansen
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Kasper Daniel Hansen
• [BioC] Create A Stranded probeAnno Object   Kasper Daniel Hansen
• [BioC] Excessive memory requirements of PING or bug?   Lars Hennig
• [BioC] outlier probes detection   Hooiveld, Guido
• [BioC] outlier probes detection   Hooiveld, Guido
• [BioC] File format for single channel analysis of Agilent microarray data with Limma?   Hooiveld, Guido
• [BioC] BiomaRt error: server down?   Lisa Hopcroft
• [BioC] DESeq   Wolfgang Huber
• [BioC] Full error messages?   Wolfgang Huber
• [BioC] edgeR outlier question   Wolfgang Huber
• [BioC] edgeR outlier question   Wolfgang Huber
• [BioC] normalize.AffyBatch.vsn with reference vsn object   Wolfgang Huber
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Wolfgang Huber
• [BioC] tilingArray normalizeByReference Data Scaling   Wolfgang Huber
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Wolfgang Huber
• [BioC] tilingArray normalizeByReference Data Scaling   Wolfgang Huber
• [BioC] DESeq error with glm.fit during estimateDispersions   Wolfgang Huber
• [BioC] Create A Stranded probeAnno Object   Wolfgang Huber
• [BioC] Human Illumina Methylation27k question   JUAN
• [BioC] normalize GFP expression by cell size and graph with densityplot   Chandra Jack
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] lumiHumanIDMapping package does not exist for windows?   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] Moderated t-test   Ekta Jain
• [BioC] Moderated t-test   Ekta Jain
• [BioC] LIMMA decideTests result zero from contrast matrix   Ekta Jain
• [BioC] Extracting topTable data from saved file   Ekta Jain
• [BioC] Moderated t-test   Ekta Jain
• [BioC] Extracting topTable data from saved file   Ekta Jain
• [BioC] edgeR: topTags   Ekta Jain
• [BioC] basics of GLMFit   chris Jhon
• [BioC] basics of GLMFit   chris Jhon
• [BioC] Questions: How to convert egt file to txt   JiangZhengyu
• [BioC] FDR calculation for expression array   JiangZhengyu
• [BioC] How to make Illumina cluster files from HapMap   JiangZhengyu
• [BioC] BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?   Martin Johnsson
• [BioC] Errors Installing Package qrqc under MacOsX   Sue Jones
• [BioC] aCGH package. Plots: X axis label problems   Sarah JugurnauthLittle
• [BioC] Job posting: Computational Biologists/Bioinformaticians, University of Cambridge, UK   Krys Kelly
• [BioC] how to rank affy probesets by their probe-effect magnitude   Leo Lahti
• [BioC] export a GappedAlignment object to a BAM file   Michael Lawrence
• [BioC] SNP detection of multiple samples   Paul Leo
• [BioC] Problem using biomaRt to retrieve human SNPs given a list of gene symbols   Yong Li
• [BioC] Genes to SNPs Tool   Yong Li
• [BioC] R IDE editor   Yue Li
• [BioC] R IDE editor   Yue Li
• [BioC] R IDE editor   Yue Li
• [BioC] R IDE editor   Yue Li
• [BioC] how to unlist a list of GappedAlignments objects   Yue Li
• [BioC] how to unlist a list of GappedAlignments objects   Yue Li
• [BioC] export a GappedAlignment object to a BAM file   Yue Li
• [BioC] export a GappedAlignment object to a BAM file   Yue Li
• [BioC] suppressMessages does not work with endoapply?   Yue Li
• [BioC] how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer   Yue Li
• [BioC] combining hgu133a and hgu133b   Steve Lianoglou
• [BioC] stable gene in microarray   Steve Lianoglou
• [BioC] basics of GLMFit   Steve Lianoglou
• [BioC] basics of GLMFit   Steve Lianoglou
• [BioC] LIMMA decideTests result zero from contrast matrix   Steve Lianoglou
• [BioC] LIMMA: plotMDS   Steve Lianoglou
• [BioC] LIMMA decideTests result zero from contrast matrix   Steve Lianoglou
• [BioC] miRNA annotation   Steve Lianoglou
• [BioC] R IDE editor   Steve Lianoglou
• [BioC] miRNA annotation   Steve Lianoglou
• [BioC] how to unlist a list of GappedAlignments objects   Steve Lianoglou
• [BioC] LIMMA decideTests result zero from contrast matrix   Steve Lianoglou
• [BioC] R IDE editor   Steve Lianoglou
• [BioC] v is for values()   Steve Lianoglou
• [BioC] v is for values()   Steve Lianoglou
• [BioC] v is for values()   Steve Lianoglou
• [BioC] v is for values()   Steve Lianoglou
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Steve Lianoglou
• [BioC] Fwd: heatmap.2 question   Steve Lianoglou
• [BioC] how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer   Steve Lianoglou
• [BioC] edgeR input and design matrix help   KJ Lim
• [BioC] edgeR : input and design matrix help   KJ Lim
• [BioC] edgeR : input and design matrix help   KJ Lim
• [BioC] edgeR : input and design matrix help   KJ Lim
• [BioC] edgeR: design matrix   KJ Lim
• [BioC] edgeR: design matrix   KJ Lim
• [BioC] edgeR: design matrix   KJ Lim
• [BioC] edgeR: topTags   KJ Lim
• [BioC] edgeR: topTags   KJ Lim
• [BioC] edgeR outlier question   Ann Loraine
• [BioC] Amplicon and exon level read counts and GC content   Michael Love
• [BioC] DESeq estimateDispersions() problem   Karl Lundén
• [BioC] Problem creating expression set.   James W. MacDonald
• [BioC] Problem with "ragene10stprobeset.db" package   James W. MacDonald
• [BioC] basics of GLMFit   James W. MacDonald
• [BioC] LIMMA decideTests result zero from contrast matrix   James W. MacDonald
• [BioC] LIMMA decideTests result zero from contrast matrix   James W. MacDonald
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   James W. MacDonald
• [BioC] FW: miRNA annotation   James W. MacDonald
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   James W. MacDonald
• [BioC] [Bioc-devel] technical and biological replicates in the same Exprset - Agi4x44   James W. MacDonald
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   James W. MacDonald
• [BioC] eset -Affy Mouse Gene 1.0 ST. Array-   James W. MacDonald
• [BioC] how to use biomaRt to retrieve probe's hgnc_symbol ... from a table of probe's chromosome coordinates?   James W. MacDonald
• [BioC] Correcting for batch effects in limma   James W. MacDonald
• [BioC] Recommend some R packages source code to read.   James W. MacDonald
• [BioC] Moderated t-test   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] error running makeProbePackage   James W. MacDonald
• [BioC] limma all adj.P.Val the same   James W. MacDonald
• [BioC] limma all adj.P.Val the same   James W. MacDonald
• [BioC] Fwd: heatmap.2 question   James W. MacDonald
• [BioC] Fwd: heatmap.2 question   James W. MacDonald
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   James W. MacDonald
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   James W. MacDonald
• [BioC] remove.dupEntrez from nsFilter{genefilter}   James W. MacDonald
• [BioC] Newbie. quantile normalization should be done on all conditions or within replicates of each condition?   James W. MacDonald
• [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?   James W. MacDonald
• [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?   James W. MacDonald
• [BioC] LIMMA: plotMDS   Aaron Mackey
• [BioC] Fwd: heatmap.2 question   Alyaa Mahmoud
• [BioC] Fwd: heatmap.2 question   Alyaa Mahmoud
• [BioC] Error loading charm   Francesco Mancuso
• [BioC] Error loading charm   Francesco Mancuso
• [BioC] Useful information about Ensembl release 67 mart databases   Thomas Maurel
• [BioC] Useful information about Ensembl release 67 mart databases   Thomas Maurel
• [BioC] limma all adj.P.Val the same   Sam McInturf
• [BioC] limma all adj.P.Val the same   Sam McInturf
• [BioC] edgeR outlier question   Simon Melov
• [BioC] edgeR outlier question   Simon Melov
• [BioC] error installing Rgraphviz   Mark Miller
• [BioC] cell cycle modeling   Anja Mirenska
• [BioC] Open PhD Position - Bioinformatics in collaboration with SAP   Amin Moghaddasi
• [BioC] Help strange GSEA error   Martin Morgan
• [BioC] Convert gene symbols to ensembl id   Martin Morgan
• [BioC] export a GappedAlignment object to a BAM file   Martin Morgan
• [BioC] Rsamtools: scanBamFlag bug?   Martin Morgan
• [BioC] Excessive memory requirements of PING or bug?   Martin Morgan
• [BioC] help with mapping statistics summary   Martin Morgan
• [BioC] GO analysis using chromosomal ranges   Martin Morgan
• [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15   Martin Morgan
• [BioC] suppressMessages does not work with endoapply?   Martin Morgan
• [BioC] Error in .testGOFrame(x, organism)   Martin Morgan
• [BioC] FastqStreamer   Martin Morgan
• [BioC] Error in .testGOFrame(x, organism)   Martin Morgan
• [BioC] Error in .testGOFrame(x, organism)   Martin Morgan
• [BioC] how to make interactive search by edgeR   Martin Morgan
• [BioC] FastqStreamer   Martin Morgan
• [BioC] Error in .testGOFrame(x, organism)   Martin Morgan
• [BioC] remove.dupEntrez from nsFilter{genefilter}   Martin Morgan
• [BioC] Amplicon and exon level read counts and GC content   Martin Morgan
• [BioC] Amplicon and exon level read counts and GC content   Martin Morgan
• [BioC] Amplicon and exon level read counts and GC content   Martin Morgan
• [BioC] samtools error   Martin Morgan
• [BioC] Cannot call ShortRead package FastqSampler from Linux   Martin Morgan
• [BioC] useDevel() not working   Michael Muratet
• [BioC] useDevel() not working   Michael Muratet
• [BioC] FOSBE 2012   Douglas Murray
• [BioC] Question regarding COA plot generated by made4 package   Valerie Obenchain
• [BioC] GRangesList filtering   Valerie Obenchain
• [BioC] GRangesList filtering   Valerie Obenchain
• [BioC] Odd behaviour with renameSeqlevels   Valerie Obenchain
• [BioC] Odd behaviour with renameSeqlevels   Valerie Obenchain
• [BioC] BSgenomes and protein sequences   Valerie Obenchain
• [BioC] BSgenomes and protein sequences: protein names   Valerie Obenchain
• [BioC] Re-send directly to BioC on miRNA annoation   Valerie Obenchain
• [BioC] Finding coding SNPs with predictCoding   Valerie Obenchain
• [BioC] BioC 2012   Valerie Obenchain
• [BioC] findOverlaps question from a newbie...   Valerie Obenchain
• [BioC] Package for doing Copy number analsysi with LOH   Valerie Obenchain
• [BioC] findOverlaps question from a newbie...   Valerie Obenchain
• [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15   Niles Oien
• [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15   Niles Oien
• [BioC] Random Forest Code   Moshe Olshansky
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Moshe Olshansky
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Moshe Olshansky
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Moshe Olshansky
• [BioC] R / Maanova: contrasts for interaction in model with 2 fixed factors   V. Oostra
• [BioC] MacOS Package installation problems   Chinedu Orekie
• [BioC] question with reading bead summary data into beadarray   Ou, Jianhong
• [BioC] question with reading bead summary data into beadarray   Ou, Jianhong
• [BioC] question about how analysis affymetrix huex st array   Ou, Jianhong
• [BioC] question about how analysis affymetrix huex st array   Ou, Jianhong
• [BioC] question about BSgenome and C.pombe genome, absent in USCS   Hervé Pagès
• [BioC] BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)   Hervé Pagès
• [BioC] questions about Overlap encodings   Hervé Pagès
• [BioC] v is for values()   Hervé Pagès
• [BioC] v is for values()   Hervé Pagès
• [BioC] BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?   Hervé Pagès
• [BioC] PWMscoreStartingAt and ambiguous subject seqs   Hervé Pagès
• [BioC] questions about Overlap encodings   Henry Paik
• [BioC] How do I find up and down regulated genes for each contrast in LIMMA?   Paul, Cristina
• [BioC] FW: How do I find up and down regulated genes for each contrast in LIMMA?   Paul, Cristina
• [BioC] Using BrainArray mappings with oligo package   Steve Piccolo
• [BioC] edgeR, comparing models   Alpesh Querer
• [BioC] LIMMA: plotMDS   Kripa R
• [BioC] LIMMA: plotMDS   Kripa R
• [BioC] limma p-value calculated how?   Kripa R
• [BioC] File format for single channel analysis of Agilent microarray data with Limma?   Parisa Razaz
• [BioC] File format for single channel analysis of Agilent microarray data with Limma?   Parisa Razaz
• [BioC] error under "hclust" for expression data   James F. Reid
• [BioC] EdgeR exactTest - treatment names determine sign of fold change   Mark Robinson
• [BioC] edgeR : input and design matrix help   Mark Robinson
• [BioC] edgeR : input and design matrix help   Mark Robinson
• [BioC] BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building   Oliver Ruebenacker
• [BioC] DESeq   Natasha Sahgal
• [BioC] DESeq   Natasha Sahgal
• [BioC] Euler diagram (Venn diagram)   Natasha Sahgal
• [BioC] Package for doing Copy number analsysi with LOH   Rajan Saini
• [BioC] MacOS Package installation problems   Michael Salbaum
• [BioC] MacOS Package installation problems   Michael Salbaum
• [BioC] MacOS Package installation problems   Michael Salbaum
• [BioC] MacOS Package installation problems   Michael Salbaum
• [BioC] GO analysis for CNVs   Yadav Sapkota
• [BioC] Query neighboring genes   Yadav Sapkota
• [BioC] Query neighboring genes   Yadav Sapkota
• [BioC] GO analysis using chromosomal ranges   Yadav Sapkota
• [BioC] Query neighboring genes   Yadav Sapkota
• [BioC] Copy Number Analysis across multiple SNP array plaforms   Ed Schwalbe
• [BioC] technical and biological replicates in the same Exprset - Agi4x44   Paola Sgadò
• [BioC] help with mapping statistics summary   Wei Shi
• [BioC] Amplicon and exon level read counts and GC content   Wei Shi
• [BioC] Amplicon and exon level read counts and GC content   Wei Shi
• [BioC] Full error messages?   Ed Siefker
• [BioC] Full error messages?   Ed Siefker
• [BioC] minfi -- now what?   Ed Siefker
• [BioC] NuIDs not found   Ed Siefker
• [BioC] beadarray package: question about processSwathData() segmentHeight and segmentWidth values   Mike Smith
• [BioC] GSEA with methylation data   Tim Smith
• [BioC] GSEA with methylation data   Tim Smith
• [BioC] Design and not estimable coefficients   Gordon K Smyth
• [BioC] Limma analyses;paired and/or factorial design?   Gordon K Smyth
• [BioC] Limma analyses;paired and/or factorial design?   Gordon K Smyth
• [BioC] basics of GLMFit   Gordon K Smyth
• [BioC] How do I find up and down regulated genes for each contrast in LIMMA?   Gordon K Smyth
• [BioC] LIMMA: plotMDS   Gordon K Smyth
• [BioC] edgeR outlier question   Gordon K Smyth
• [BioC] technical and biological replicates in the same Exprset - Agi4x44   Gordon K Smyth
• [BioC] Moderated t-test   Gordon K Smyth
• [BioC] Building specific Ortoghonal contrasts in LIMMA   Gordon K Smyth
• [BioC] edgeR outlier question   Gordon K Smyth
• [BioC] edgeR outlier question   Gordon K Smyth
• [BioC] Building specific Ortoghonal contrasts in LIMMA   Gordon K Smyth
• [BioC] how to design matrix by edgeR   Gordon K Smyth
• [BioC] how to design matrix by edgeR   Gordon K Smyth
• [BioC] how to design matrix by edgeR   Gordon K Smyth
• [BioC] How to open the edgeR Users Guide within R?   Gordon K Smyth
• [BioC] edgeR, comparing models   Gordon K Smyth
• [BioC] non-integer counts for edgeR   Gordon K Smyth
• [BioC] edgeR, comparing models   Gordon K Smyth
• [BioC] non-integer counts for edgeR   Gordon K Smyth
• [BioC] EdgeR: problem with large logFC value   Gordon K Smyth
• [BioC] technical and biological replicates in the same Exprset - Agi4x44   Gordon K Smyth
• [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)   Gordon K Smyth
• [BioC] Expt. design question on optimal number of replicates (in edgeR or elsewhere)   Gordon K Smyth
• [BioC] edgeR: design matrix   Gordon K Smyth
• [BioC] File format for single channel analysis of Agilent microarray data with Limma?   Gordon K Smyth
• [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)   Gordon K Smyth
• [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)   Gordon K Smyth
• [BioC] Help with adSplit package   Luz Mayela Soto
• [BioC] EdgeR exactTest - treatment names determine sign of fold change   Spollen, William G.
• [BioC] EdgeR exactTest - treatment names determine sign of fold change   Spollen, William G.
• [BioC] tilingArray normalizeByReference Data Scaling   Dario Strbenac
• [BioC] tilingArray normalizeByReference Data Scaling   Dario Strbenac
• [BioC] iSeq Peak Position   Dario Strbenac
• [BioC] Create A Stranded probeAnno Object   Dario Strbenac
• [BioC] Create A Stranded probeAnno Object   Dario Strbenac
• [BioC] Create A Stranded probeAnno Object   Dario Strbenac
• [BioC] Create A Stranded probeAnno Object   Dario Strbenac
• [BioC] GRanges Constructor With seqlengths   Dario Strbenac
• [BioC] GRanges Constructor With seqlengths   Dario Strbenac
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Marie Sémon
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Marie Sémon
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Marie Sémon
• [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis   Marie Sémon
• [BioC] normalize.AffyBatch.vsn with reference vsn object   R Tagett
• [BioC] normalize.AffyBatch.vsn with reference vsn object   R Tagett
• [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?   Y-h. Taguchi
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] Amplicon and exon level read counts and GC content   Yu Chuan Tai
• [BioC] samtools error   Yu Chuan Tai
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   Juan Fernández Tajes
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   Juan Fernández Tajes
• [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray   Juan Fernández Tajes
• [BioC] Human Illumina Methylation27k question   Juan Fernández Tajes
• [BioC] Human Illumina Methylation27k question   Juan Fernández Tajes
• [BioC] lumiHumanIDMapping package does not exist for windows?   Dan Tenenbaum
• [BioC] Error loading charm   Dan Tenenbaum
• [BioC] lumiHumanIDMapping package does not exist for windows?   Dan Tenenbaum
• [BioC] lumiHumanIDMapping package does not exist for windows?   Dan Tenenbaum
• [BioC] lumiHumanIDMapping package does not exist for windows?   Dan Tenenbaum
• [BioC] Excessive memory requirements of PING or bug?   Dan Tenenbaum
• [BioC] Excessive memory requirements of PING or bug?   Dan Tenenbaum
• [BioC] 'citation("RBGL")' command produces package not found error   Dan Tenenbaum
• [BioC] GEOquery loading error   Dan Tenenbaum
• [BioC] GEOquery loading error   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] error installing Rgraphviz   Dan Tenenbaum
• [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] topGO dependency: Rgrapphviz   Dan Tenenbaum
• [BioC] topGO dependency: Rgrapphviz   Dan Tenenbaum
• [BioC] MacOS Package installation problems   Dan Tenenbaum
• [BioC] topGO dependency: Rgrapphviz   Thompson, Kevin
• [BioC] topGO dependency: Rgrapphviz   Thompson, Kevin
• [BioC] Human Illumina Methylation27k question   Djie Tjwan Thung
• [BioC] Human Illumina Methylation27k question   Djie Tjwan Thung
• [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15   Djie Tjwan Thung
• [BioC] minfi -- now what?   Tim Triche, Jr.
• [BioC] NuIDs not found   Tim Triche, Jr.
• [BioC] problem with makeFeatureDbFromUCSC and snp135Common track   Tim Triche, Jr.
• [BioC] minfi -- now what?   Tim Triche, Jr.
• [BioC] LIMMA: plotMDS   Tim Triche, Jr.
• [BioC] LIMMA: plotMDS   Tim Triche, Jr.
• [BioC] v is for values()   Tim Triche, Jr.
• [BioC] v is for values()   Tim Triche, Jr.
• [BioC] v is for values()   Tim Triche, Jr.
• [BioC] v is for values()   Tim Triche, Jr.
• [BioC] 450K annotation: discrepancy between GEO GPL and Bioconductor annotation   Tim Triche, Jr.
• [BioC] Query neighboring genes   Tim Triche, Jr.
• [BioC] Query neighboring genes   Tim Triche, Jr.
• [BioC] Query neighboring genes   Tim Triche, Jr.
• [BioC] Is there a package that can map CBS result to original probe ID or gene ID?   Tim Triche, Jr.
• [BioC] GSEA with methylation data   Tim Triche, Jr.
• [BioC] Euler diagram (Venn diagram)   Tim Triche, Jr.
• [BioC] non-integer counts for edgeR   Tim Triche, Jr.
• [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)   Tim Triche, Jr.
• [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)   Tim Triche, Jr.
• [BioC] BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building   Tim Triche, Jr.
• [BioC] Recommend some R packages source code to read.   Fabrice Tourre
• [BioC] GRangesList filtering   Halian Vilela
• [BioC] pdInfoBuilder: coreMps   Mike Walter
• [BioC] pdInfoBuilder: coreMps   Mike Walter
• [BioC] edgeR output figures   Wang, Li
• [BioC] Moderated t-test   Wang, Li
• [BioC] error under "hclust" for expression data   Wang, Li
• [BioC] SNP detection of multiple samples   Wang, Li
• [BioC] Fwd: heatmap.2 question   Wang, Li
• [BioC] SNP detection of multiple samples   Wang, Li
• [BioC] edgeR: topTags   Wang, Li
• [BioC] limma p-value calculated how?   David Westergaard
• [BioC] 'citation("RBGL")' command produces package not found error   Jeremiah Willcock
• [BioC] 'citation("RBGL")' command produces package not found error   Jeremiah Willcock
• [BioC] 'citation("RBGL")' command produces package not found error   Jeremiah Willcock
• [BioC] LIMMA: plotMDS   Wu, Di
• [BioC] GSEA with methylation data   Wu, Di
• [BioC] miRNA annotation   Wu, Huiyun
• [BioC] miRNA annotation   Wu, Huiyun
• [BioC] Re-send directly to BioC on miRNA annoation   Wu, Huiyun
• [BioC] FW: miRNA annotation   Wu, Huiyun
• [BioC] FW: miRNA annotation   Wu, Huiyun
• [BioC] Re-send directly to BioC on miRNA annoation   Wu, Huiyun
• [BioC] miRNA and other small RNAs   Wu, Huiyun
• [BioC] easyRNASeq Error in counting from C.elegans   Yonggan Wu
• [BioC] easyRNASeq Error in counting from C.elegans   Yonggan Wu
• [BioC] PWMscoreStartingAt and ambiguous subject seqs   Janet Young
• [BioC] PWMscoreStartingAt and ambiguous subject seqs   Janet Young
• [BioC] PWMscoreStartingAt and ambiguous subject seqs   Janet Young
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] error running makeProbePackage   Zhang, Jian
• [BioC] GEOquery loading error   Zhang, Jian
• [BioC] GEOquery loading error   Zhang, Jian
• [BioC] Excessive memory requirements of PING or bug?   Xuekui Zhang
• [BioC] question regarding ChIPPeakAnno use   Zhu, Lihua (Julie)
• [BioC] BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)   Zhu, Lihua (Julie)
• [BioC] GO analysis for CNVs   Zhu, Lihua (Julie)
• [BioC] ChIPPeakAnno query (overlaps)   Zhu, Lihua (Julie)
• [BioC] BiomaRt returns empty set for getBM for celegans miRNA   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno annotatePeakInBatch   Zhu, Lihua (Julie)
• [BioC] ChIPPeakAnno query (overlaps)   Zhu, Lihua (Julie)
• [BioC] Query neighboring genes   Zhu, Lihua (Julie)
• [BioC] Query neighboring genes   Zhu, Lihua (Julie)
• [BioC] Query neighboring genes   Zhu, Lihua (Julie)
• [BioC] BSgenomes and protein sequences   Zybaylov, Boris L
• [BioC] BSgenomes and protein sequences: protein names   Zybaylov, Boris L
• [BioC] biomart error returning data   Alasdair Jubb [guest]
• [BioC] GOSim yeast   Fred Hoffman [guest]
• [BioC] GEOquery loading error   Jian Zhang [guest]
• [BioC] remove.dupEntrez from nsFilter{genefilter}   Klemens Vierlinger [guest]
• [BioC] How to identify DE genes by comparing two groups where one contains a single array data   Lei Li [guest]
• [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15   Niles Oien [guest]
• [BioC] File format for single channel analysis of Agilent microarray data with Limma?   Parisa [guest]
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   Simone [guest]
• [BioC] beadarray package - analysis of bead summary level data   Yehudit Hasin [guest]
• [BioC] how to make interactive search by edgeR   narges [guest]
• [BioC] Gene Ratios   somnath bandyopadhyay
• [BioC] Euler diagram (Venn diagram)   pankaj borah
• [BioC] methylumi on Infiniium27k idat files   chris briggs
• [BioC] eset -Affy Mouse Gene 1.0 ST. Array-   alessandro brozzi
• [BioC] eset -Affy Mouse Gene 1.0 ST. Array-   alessandro brozzi
• [BioC] fitting growth curve   alessandro brozzi
• [BioC] fitting growth curve   alessandro brozzi
• [BioC] fitting growth curve   alessandro brozzi
• [BioC] how to use biomaRt to retrieve probe's hgnc_symbol ... from a table of probe's chromosome coordinates?   ying chen
• [BioC] Is there a package that can map CBS result to original probe ID or gene ID?   ying chen
• [BioC] DESeq error with glm.fit during estimateDispersions   chris_utah
• [BioC] design and contrast matrix for limma time series without replicates   shao chunxuan
• [BioC] Adding a column to phenoData dataframe   ieee529 contact
• [BioC] question about how analysis affymetrix huex st array   cstrato
• [BioC] question about how analysis affymetrix huex st array   cstrato
• [BioC] Question regarding COA plot generated by made4 package   aedin culhane
• [BioC] Question regarding MADE4 graphs   aedin culhane
• [BioC] problem with edgeR smearPlot function   capricy gao
• [BioC] edgeR outlier question   alessandro.guffanti at genomnia.com
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")   ecsi at gmx.net
• [BioC] findOverlaps question from a newbie...   gowtham
• [BioC] Expt. design question on optimal number of replicates (in edgeR or else where)   gowtham
• [BioC] Expt. design question on optimal number of replicates (in edgeR or elsewhere)   gowtham
• [BioC] findOverlaps question from a newbie...   gowtham
• [BioC] Limma analyses;paired and/or factorial design?   john herbert
• [BioC] FDR calculation for expression array   wenhuo hu
• [BioC] R IDE editor   wenhuo hu
• [BioC] GSEA with methylation data   wenhuo hu
• [BioC] beadarray package - analysis of bead summary level data   wenhuo hu
• [BioC] outlier probes detection   andrea.grilli at ior.it
• [BioC] outlier probes detection   andrea.grilli at ior.it
• [BioC] outlier probes detection   andrea.grilli at ior.it
• [BioC] problem with large logFC value   sgonzalez at ira.cinvestav.mx
• [BioC] EdgeR: problem with large logFC value   sgonzalez at ira.cinvestav.mx
• [BioC] Correcting for batch effects in limma   khadeeja ismail
• [BioC] Correcting for batch effects in limma   khadeeja ismail
• [BioC] Outcome~predictor model evaluation, repeated measurements   rad mac
• [BioC] Convert gene symbols to ensembl id   michelle_low
• [BioC] Convert gene symbols to ensembl id   michelle_low
• [BioC] Extracting topTable data from saved file   michelle_low
• [BioC] TEQC see all the reads with a given coverage   nathalie
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] Error in .testGOFrame(x, organism)   omranian
• [BioC] how to get plant taxonomy   wang peter
• [BioC] how to design matrix by edgeR   wang peter
• [BioC] how to design matrix by edgeR   wang peter
• [BioC] how to design a model matrix   wang peter
• [BioC] how to design matrix by edgeR   wang peter
• [BioC] DEXSeq filtering   mali salmon
• [BioC] DEXSeq filtering   mali salmon
• [BioC] Cannot call ShortRead package FastqSampler from Linux   talshay
• [BioC] beadarray package: question about processSwathData() segmentHeight and segmentWidth values   bzguan at ucdavis.edu
• [BioC] beadarray package: problem finding Illumina annotation for Human660w_quad bead chip   bzguan at ucdavis.edu
• [BioC] May-July 2012 ***R/S-PLUS Courses***by XLSolutions Corp at 9 USA locations   sue at xlsolutions-corp.com

Last message date: Thu May 31 23:53:42 CEST 2012
Archived on: Fri Jun 1 00:50:56 CEST 2012

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