April 2011 Archives by author

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Starting: Fri Apr 1 00:36:47 CEST 2011
Ending: Sat Apr 30 12:53:12 CEST 2011
Messages: 526

• [BioC] GEOsubmission help request   Manca Marco (PATH)
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   Naomi Altman
• [BioC] limma   Naomi Altman
• [BioC] what to do with microarray outliers?   Naomi Altman
• [BioC] Limma, eBayes different sample size of groups and adjustment   Naomi Altman
• [BioC] gff files: how to tell if right-open interval convention used?   Simon Anders
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   Simon Anders
• [BioC] deseq for multiple groups with no replicate   Simon Anders
• [BioC] deseq for multiple groups with no replicate   Simon Anders
• [BioC] GO enrichment and pathways   Radhouane Aniba
• [BioC] DESeq - non-differential expression   Christophe Antoniewski
• [BioC] karyotype annotation   Nandini B
• [BioC] karyotype annotation   Nandini B
• [BioC] karyotype annotation   Nandini B
• [BioC] Converting list to a matrix   Pankaj Barah
• [BioC] Converting list to a matrix   Pankaj Barah
• [BioC] How to split data faster?   Christoph Bartenhagen
• [BioC] Converting list to a matrix   Carlos J. Gil Bellosta
• [BioC] Converting list to a matrix   Carlos J. Gil Bellosta
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Henrik Bengtsson
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Henrik Bengtsson
• [BioC] customCDF name not recognized and switched to Affy CDF   Yair Benita
• [BioC] Desing matrix in limma   Dario Beraldi
• [BioC] Desing matrix in limma   Dario Beraldi
• [BioC] RNASeq: normalization issues   Biase, Fernando
• [BioC] problems with estimateGLMTrendedDisp()   Biase, Fernando
• [BioC] Problems with VST in lumi   Michal Blazejczyk
• [BioC] system() command in R   Markus Boenn
• [BioC] read gz compressed wig files?   Hamid Bolouri
• [BioC] read gz compressed wig files?   Hamid Bolouri
• [BioC] read gz compressed wig files?   Hamid Bolouri
• [BioC] read gz compressed wig files?   Hamid Bolouri
• [BioC] what to do with microarray outliers?   Theresa Brandt
• [BioC] arrayQualityMetrics with R 2.13.0 fails   Eric Bremer
• [BioC] Normalising to Agilent controls in a two-colour experiment   Daniel Brewer
• [BioC] Grofit script   Brinsmade, Shaun R.
• [BioC] RNASeq: normalization issues   Vince S. Buffalo
• [BioC] healthcare lists, business lists, consumer lists, professional lists and more   Estella Calderon
• [BioC] hgu133plus2hsentrezgprobe install problem   Vincent Carey
• [BioC] system() command in R   Vincent Carey
• [BioC] Retrieving a subset from normalized microarray data for differential test in R package, Limma   Vincent Carey
• [BioC] Structural variations analysis   Vincent Carey
• [BioC] Biobase 2.8 with R 2.13.0 fails on my Mac   Vincent Carey
• [BioC] RMAPPER and whole genome TFBS information   Vincent Carey
• [BioC] problem installing affyPLMpackage   Vincent Carey
• [BioC] Concatenating or merging two or more ExpressionSet objects   Vincent Carey
• [BioC] GOstats problem with output   Marc Carlson
• [BioC] GenomicFeatures: Unable to save TranscriptDb object   Marc Carlson
• [BioC] GO enrichment and pathways   Marc Carlson
• [BioC] Bioconductor Digest, Vol 98, Issue 6   Marc Carlson
• [BioC] GenomicRangesUseCases Manual :: Typo?   Marc Carlson
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Marc Carlson
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Marc Carlson
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Marc Carlson
• [BioC] Create an non-mainstream organism-specific database for ChIP-chip analysis   Marc Carlson
• [BioC] Bimap and flatten()   Marc Carlson
• [BioC] Bimap and flatten()   Marc Carlson
• [BioC] differences between "manual" boxplots and "standard" boxplots of a oligo object   Benilton Carvalho
• [BioC] Output IUPAC genotypes from oligo?   Benilton Carvalho
• [BioC] pdInfoBuilder   Benilton Carvalho
• [BioC] Problem with pdInfoBuilder   Benilton Carvalho
• [BioC] identifying consistently expressed genes between replicates   Florence Cavalli
• [BioC] Converting list to a matrix   Arunava Chakravartty
• [BioC] BioC in the cloud (was Re: [Bioc-devel] Bioconductor 2.8 is released)   Brad Chapman
• [BioC] multiple hits with countOverlaps function   Mete Civelek
• [BioC] Weighted counts in countGenomicOverlaps   Mete Civelek
• [BioC] collapsing redundant probe sets of Affymetrix Chips   Mete Civelek
• [BioC] Affymetrix 250K SNP aCGH   Djork-Arne Clevert
• [BioC] arch=i386   Stat Consult
• [BioC] Script to save plots in Pdf format ( DNAcopy)   Nathalie Conte
• [BioC] rtracklayer gff import   Cook, Malcolm
• [BioC] Limma   Kevin R. Coombes
• [BioC] pa.calls-function in package "panp"   Kyle R Covington
• [BioC] arrayQualityMetrics   Mark Cowley
• [BioC] arrayQualityMetrics   Mark Cowley
• [BioC] seqnames on dbSNP object error   Mark Cowley
• [BioC] seqnames on dbSNP object error   Mark Cowley
• [BioC] Custom cdf 14.1.0 is released   Manhong Dai
• [BioC] How to read in log2 ratio data   Peter Davidsen
• [BioC] lmFit only deals with numerical values (data matrix object)?   Peter Davidsen
• [BioC] lmFit only deals with numerical values (data matrix object)?   Peter Davidsen
• [BioC] lmFit only deals with numerical values (data matrix object)?   Sean Davis
• [BioC] lmFit only deals with numerical values (data matrix object)?   Sean Davis
• [BioC] Converting list to a matrix   Sean Davis
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Sean Davis
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Sean Davis
• [BioC] I'm confused about LIMMA statistics   Sean Davis
• [BioC] convertion from SAM to BAM   Sean Davis
• [BioC] question about topTable in limma   Sean Davis
• [BioC] Converting list to a matrix   Day, Roger S
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Diego Diez
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Diego Diez
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Diego Diez
• [BioC] BrainArray custom CDF repository missing in biocReposList()   Diego Diez
• [BioC] Script to save plots in Pdf format ( DNAcopy)   René Dreos
• [BioC] Limma   Jenny Drnevich
• [BioC] what to do with microarray outliers?   Jenny Drnevich
• [BioC] biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?   Duke
• [BioC] biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?   Duke
• [BioC] summarized expression values from beadarray versus GenomeStudio   Mark Dunning
• [BioC] summarized expression values from beadarray versus GenomeStudio   Mark Dunning
• [BioC] TLR4 in illuminaHumanv3.db   Mark Dunning
• [BioC] problem with biomaRt package using mart "snps", dataset "hsapiens_structvar", attribute "description"   Steffen Durinck
• [BioC] problem with biomaRt package using mart "snps", dataset "hsapiens_structvar", attribute "description"   Steffen Durinck
• [BioC] using BioMart to query UniProt identifiers   Steffen Durinck
• [BioC] biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?   Steffen Durinck
• [BioC] Compatibility of Biorad cfx files to HTqPCR?   Heidi Dvinge
• [BioC] image size - How to make bigger images   Heidi Dvinge
• [BioC] image size - How to make bigger images   Heidi Dvinge
• [BioC] Help on references for R Bioconductor   Heidi Dvinge
• [BioC] flowCore split function with curv2Filter and population argument   Greg Finak
• [BioC] Rgraphviz weight attributes   Robert M. Flight
• [BioC] GOstats problem with output   Robert M. Flight
• [BioC] GOstats problem with output   Robert M. Flight
• [BioC] error in hugene10sttranscriptcluster   Javier Pérez Florido
• [BioC] error in hugene10sttranscriptcluster   Javier Pérez Florido
• [BioC] error in hugene10sttranscriptcluster   Javier Pérez Florido
• [BioC] differences between "manual" boxplots and "standard" boxplots of a oligo object   Javier Pérez Florido
• [BioC] two questions regarding Human Gene 1.0 ST arrays   Javier Pérez Florido
• [BioC] two questions regarding Human Gene 1.0 ST arrays   Javier Pérez Florido
• [BioC] two questions regarding Human Gene 1.0 ST arrays   Javier Pérez Florido
• [BioC] Human Gene array data analysis workflow   Javier Pérez Florido
• [BioC] Human Gene array data analysis workflow   Javier Pérez Florido
• [BioC] Retrieving a subset from normalized microarray data for differential test in R package, Limma   Amos Folarin
• [BioC] image size - How to make bigger images   Amos Folarin
• [BioC] Whole genome searching of 100bp "D" sequence   Amos Folarin
• [BioC] gff files: how to tell if right-open interval convention used?   Julien Gagneur
• [BioC] Chip-Seq tag density plot   Eva Benito Garagorri
• [BioC] Bimap and flatten()   Laurent Gautier
• [BioC] Bimap and flatten()   Laurent Gautier
• [BioC] convertion from SAM to BAM   Paul Geeleher
• [BioC] Limma, eBayes different sample size of groups and adjustment   Paul Geeleher
• [BioC] Bioconductor AMI Amazon EC2 help   David Gibbs
• [BioC] R/Bioc workshops at UC Riverside   Thomas Girke
• [BioC] exonmap problems with rma normalization   Gomez Moruno, Antonio
• [BioC] problems with Affymetrix probes id using exonmap and xmapcore   Gomez Moruno, Antonio
• [BioC] flowTrack error: package ‘flowTrack’ is not available   Nishant Gopalakrishnan
• [BioC] GRanges nearest problem   Nishant Gopalakrishnan
• [BioC] rtracklayer - export.wig issue   Lavinia Gordon
• [BioC] rtracklayer - export.wig issue   Lavinia Gordon
• [BioC] [Bioc-sig-seq] Bioconductor 2.8 is released   Ivan Gregoretti
• [BioC] [Bioc-sig-seq] Bioconductor 2.8 is released   Ivan Gregoretti
• [BioC] [Bioc-sig-seq] Bioconductor 2.8 is released   Ivan Gregoretti
• [BioC] flowCore split function with curv2Filter and population argument   Aric Gregson
• [BioC] hgu133plus2hsentrezgprobe install problem   Obi Griffith
• [BioC] hgu133plus2hsentrezgprobe install problem   Obi Griffith
• [BioC] Read.maimages with Mac OS X v.10.6 Snow Leopard   Priscila Grynberg
• [BioC] Read.maimages with Mac OS X v.10.6 Snow Leopard - SessionInfo update   Priscila Grynberg
• [BioC] Read.maimages with Mac OS X v.10.6 Snow Leopard - SessionInfo update   Priscila Grynberg
• [BioC] question about the aroma.affymetrix   Xiaowei Guan
• [BioC] Script to save plots in Pdf format ( DNAcopy)   Thomas Hampton
• [BioC] How to read in log2 ratio data   Thomas Hampton
• [BioC] Script to save plots in Pdf format ( DNAcopy)   Kasper Daniel Hansen
• [BioC] multiple hits with countOverlaps function   Kasper Daniel Hansen
• [BioC] Rsubread alingner   Kasper Daniel Hansen
• [BioC] GO enrichment and pathways   Yuan Hao
• [BioC] removal of affymetrix control probes from ExpressionSet   Yuan Hao
• [BioC] DESeq - non-differential expression   Thomas J Hardcastle
• [BioC] Concatenating or merging two or more ExpressionSet objects   Christos Hatzis
• [BioC] normalize different data sets against common reference   Andreas Heider
• [BioC] redundant probe sets in Affymetrix HG-U219   Andreas Heider
• [BioC] custom CDF files for non-redundant transcript/gene annotation that is consistent over several platforms   Andreas Heider
• [BioC] collapsing redundant probe sets of Affymetrix Chips   Andreas Heider
• [BioC] summarized expression values from beadarray versus GenomeStudio   Ina Hoeschele
• [BioC] summarized expression values from beadarray versus GenomeStudio   Ina Hoeschele
• [BioC] summarized expression values from beadarray versus GenomeStudio   Ina Hoeschele
• [BioC] summarized expression values from beadarray versus GenomeStudio   Ina Hoeschele
• [BioC] Compatibility of Biorad cfx files to HTqPCR?   Hooiveld, Guido
• [BioC] rtracklayer gff import   Hans-Rudolf Hotz
• [BioC] problem with biomaRt package using mart "snps", dataset "hsapiens_structvar", attribute "description"   Wolfgang Huber
• [BioC] arrayQualityMetrics   Wolfgang Huber
• [BioC] deseq for multiple groups with no replicate   Wolfgang Huber
• [BioC] edgeR and deSEQ glms   Wolfgang Huber
• [BioC] arrayQualityMetrics   Wolfgang Huber
• [BioC] arrayQualityMetrics   Wolfgang Huber
• [BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?   Wolfgang Huber
• [BioC] Limma   Wolfgang Huber
• [BioC] limma   Wolfgang Huber
• [BioC] conditional replace column values with values from a different column   Wolfgang Huber
• [BioC] limma   Wolfgang Huber
• [BioC] image size - How to make bigger images   Wolfgang Huber
• [BioC] DESeq - non-differential expression   Wolfgang Huber
• [BioC] deseq for multiple groups with no replicate   Wolfgang Huber
• [BioC] deseq for multiple groups with no replicate   Wolfgang Huber
• [BioC] RNASeq: normalization issues   Wolfgang Huber
• [BioC] Extracting Data from SimpleRleViewsList   Lakshmanan Iyer
• [BioC] Can't reproduce assessment data included in affycomp package   Harris A. Jaffee
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Saurin D. Jani
• [BioC] how to merge two or several DNAStringSet objects   Mao Jianfeng
• [BioC] Affymetrix 250K SNP aCGH   Adrian Johnson
• [BioC] I'm confused about LIMMA statistics   Amy Johnson
• [BioC] [maSigPro] Splitting data - how?   "Maciej Jończyk"
• [BioC] [Mfuzz] Error in cmeans(exprs(eset)   Maciej Jończyk
• [BioC] [Mfuzz] Error in cmeans(exprs(eset)   Maciej Jończyk
• [BioC] prepare data matrix for siggenes   Maciej Jończyk
• [BioC] [Mfuzz] y-axis values   Maciej Jończyk
• [BioC] GenomicFeatures: Unable to save TranscriptDb object   KORIR, PAUL
• [BioC] GenomicRangesUseCases Manual :: Typo?   KORIR, PAUL
• [BioC] RMAPPER and whole genome TFBS information   Ravi Karra
• [BioC] Paired tests using limma and beadarray   Moritz Kebschull
• [BioC] biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?   Rhoda Kinsella
• [BioC] beadarray: Running BASH for 120 sections   Gavin Koh
• [BioC] beadarray: Running BASH for 120 sections   Gavin Koh
• [BioC] beadarray: Running BASH for 120 sections   Gavin Koh
• [BioC] beadarray: Running BASH for 120 sections   Gavin Koh
• [BioC] TLR4 in illuminaHumanv3.db   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Gavin Koh
• [BioC] GEOsubmission help request   Alexandre Kuhn
• [BioC] edgeR- plotSmear   Sridhara Gupta Kunjeti
• [BioC] edgeR- plotSmear   Sridhara Gupta Kunjeti
• [BioC] edgeR- plotSmear   Sridhara Gupta Kunjeti
• [BioC] Bioconductor Digest, Vol 98, Issue 6   UnASM Lab_bi
• [BioC] backgroundcorrection in beadarray   Hajar Hassani Lahsinoui
• [BioC] gsea (gene set enrichment analysis) for ranked lists   Asta Laiho
• [BioC] RE : gsea (gene set enrichment analysis) for ranked lists   Asta Laiho
• [BioC] rtracklayer - export.wig issue   Michael Lawrence
• [BioC] read gz compressed wig files?   Michael Lawrence
• [BioC] rtracklayer - export.wig issue   Michael Lawrence
• [BioC] read gz compressed wig files?   Michael Lawrence
• [BioC] How to split data faster?   Michael Lawrence
• [BioC] multiple hits with countOverlaps function   Michael Lawrence
• [BioC] how to merge two or several DNAStringSet objects   Michael Lawrence
• [BioC] rtracklayer gff import   Michael Lawrence
• [BioC] multiple hits with countOverlaps function   Michael Lawrence
• [BioC] rtracklayer   Michael Lawrence
• [BioC] Concatenating or merging two or more ExpressionSet objects   Richard Leduc
• [BioC] read gz compressed wig files?   Steve Lianoglou
• [BioC] arrayQualityMetrics   Steve Lianoglou
• [BioC] edgeR glm   Steve Lianoglou
• [BioC] Limma   Steve Lianoglou
• [BioC] multiple hits with countOverlaps function   Steve Lianoglou
• [BioC] GO enrichment and pathways   Steve Lianoglou
• [BioC] microarray analysis query   Steve Lianoglou
• [BioC] [Bioc-devel] Bioconductor 2.8 is released   Steve Lianoglou
• [BioC] (no subject)   Steve Lianoglou
• [BioC] R for normalizing gene length for next-gene sequencing data   Steve Lianoglou
• [BioC] M values; and dist functions   Steve Lianoglou
• [BioC] convertion from SAM to BAM   Steve Lianoglou
• [BioC] M values; and dist functions   Steve Lianoglou
• [BioC] ENVISIONQuery package   Alex Lisovich
• [BioC] ENVISIONQuery package   Alex Lisovich
• [BioC] inconsistency between GRangesList and transcriptDB object.   Jason Lu
• [BioC] Create an non-mainstream organism-specific database for ChIP-chip analysis   Olivier Lucas
• [BioC] How to get R plots with FastRweb   MLSC MANIPAL
• [BioC] Problem with pdInfoBuilder   Michael MOZAR
• [BioC] error in hugene10sttranscriptcluster   James MacDonald
• [BioC] merged affy 430 A&B   James W. MacDonald
• [BioC] Limma   James W. MacDonald
• [BioC] How to read in log2 ratio data   James W. MacDonald
• [BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?   James W. MacDonald
• [BioC] Limma   James W. MacDonald
• [BioC] merged affy 430 A&B   James W. MacDonald
• [BioC] What's the difference of the two approach for two groups in limma?   James W. MacDonald
• [BioC] Converting list to a matrix   James W. MacDonald
• [BioC] simpleafy plots   James W. MacDonald
• [BioC] Desing matrix in limma   James W. MacDonald
• [BioC] redundant probe sets in Affymetrix HG-U219   James W. MacDonald
• [BioC] customCDF name not recognized and switched to Affy CDF   James W. MacDonald
• [BioC] error in hugene10sttranscriptcluster   James W. MacDonald
• [BioC] Paired tests using limma and beadarray   James W. MacDonald
• [BioC] Adapted clusterStab package   James W. MacDonald
• [BioC] error in hugene10sttranscriptcluster   James W. MacDonald
• [BioC] Limma   Seraya Maouche
• [BioC] Limma   Seraya Maouche
• [BioC] Limma   Seraya Maouche
• [BioC] limma   Seraya Maouche
• [BioC] Pathway Analyis for C-difficile microarrays   Claus Mayer
• [BioC] Creating 2 Gaussian Probability Density Function   Matthew McCall
• [BioC] select present probes   Matthew McCall
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   Davis McCarthy
• [BioC] edgeR- plotSmear   Davis McCarthy
• [BioC] edgeR- plotSmear   Davis McCarthy
• [BioC] problem installing affyPLMpackage   Matthew McCormack
• [BioC] problem installing affyPLMpackage   Matthew McCormack
• [BioC] collapsing redundant probe sets of Affymetrix   Swapna Menon
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] arrayQualityMetrics   Guillaume Meurice
• [BioC] Re(surrecting): [Bioc-sig-seq] Rsamtools countBam labeling   Martin Morgan
• [BioC] read gz compressed wig files?   Martin Morgan
• [BioC] RE : gsea (gene set enrichment analysis) for ranked lists   Martin Morgan
• [BioC] convertion from SAM to BAM   Martin Morgan
• [BioC] BioC 2011 -- Where Software and Biology Connect, Seattle, WA July 28-29   Martin Morgan
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Vladimir Morozov
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Vladimir Morozov
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Vladimir Morozov
• [BioC] [Bioc-sig-seq] Bioconductor 2.8 is released   João Moura
• [BioC] Rsubread alingner   João Moura
• [BioC] Rsubread alingner   João Moura
• [BioC] Rsubread alingner   João Moura
• [BioC] convertion from SAM to BAM   João Moura
• [BioC] convertion from SAM to BAM   João Moura
• [BioC] convertion from SAM to BAM   João Moura
• [BioC] Rsubread alingner   João Moura
• [BioC] RNASeq: normalization issues   João Moura
• [BioC] Questions about package DESeq   Mr.B
• [BioC] GRanges nearest problem   Mueller, Arne
• [BioC] Limma, eBayes different sample size of groups and adjustment   Babara Mueller
• [BioC] edgeR and deSEQ glms   Shreyartha Mukherjee
• [BioC] edgeR and deSEQ glms   Shreyartha Mukherjee
• [BioC] edgeR glm   Shreyartha Mukherjee
• [BioC] edgeR glm   Shreyartha Mukherjee
• [BioC] edgeR glm   Shreyartha Mukherjee
• [BioC] RE : gsea (gene set enrichment analysis) for ranked lists   Simon Noël
• [BioC] GRanges nearest problem   Valerie Obenchain
• [BioC] multiple hits with countOverlaps function   Valerie Obenchain
• [BioC] multiple hits with countOverlaps function   Valerie Obenchain
• [BioC] Weighted counts in countGenomicOverlaps   Valerie Obenchain
• [BioC] Weighted counts in countGenomicOverlaps   Valerie Obenchain
• [BioC] Bioinformatics Post-doc in Melbourne   Alicia Oshlack
• [BioC] How to split data faster?   Ou, Jianhong
• [BioC] What's the difference of the two approach for two groups in limma?   Ou, Jianhong
• [BioC] What's the difference of the two approach for two groups in limma?   Ou, Jianhong
• [BioC] gff files: how to tell if right-open interval convention used?   Pages, Herve
• [BioC] gff files: how to tell if right-open interval convention used?   Hervé Pagès
• [BioC] girafe issues - no interval overlap   Hervé Pagès
• [BioC] GenomicFeatures: Unable to save TranscriptDb object   Hervé Pagès
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Hervé Pagès
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Hervé Pagès
• [BioC] conditional replace column values with values from a different column   Hervé Pagès
• [BioC] seqnames on dbSNP object error   Hervé Pagès
• [BioC] EBarrays question   Hervé Pagès
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Gregoire Pau
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Gregoire Pau
• [BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),   Gregoire Pau
• [BioC] Structural variations analysis   Richard Pearson
• [BioC] flowTrack error: package ‘flowTrack’ is not available   Louis Peperzak
• [BioC] flowTrack error: package ‘flowTrack’ is not available   Louis Peperzak
• [BioC] how to select multiple columns in read.flowSet   Louis Peperzak
• [BioC] identifying consistently expressed genes between replicates   Wendy Qiao
• [BioC] identifying consistently expressed genes between replicates   Wendy Qiao
• [BioC] identifying consistently expressed genes between replicates   Wendy Qiao
• [BioC] select present probes   Wendy Qiao
• [BioC] Adapted clusterStab package   Wendy Qiao
• [BioC] SVM Patent Discussion   Hsu Qinghua
• [BioC] SVM Patent Discussion   XU Qinghua
• [BioC] Package Icens_1.24.0.tar.gz has been built for Windows   Uwe.Ligges at R-Project.org
• [BioC] Package gpls_1.24.0.tar.gz has been built for Windows   Uwe.Ligges at R-Project.org
• [BioC] using BioMart to query UniProt identifiers   Wolfgang RAFFELSBERGER
• [BioC] Regarding the ChIPpeakAnno Package   Ayush Raman
• [BioC] Informations about DESeq package   Bruno Roman
• [BioC] microarray analysis query   Umme Rummana
• [BioC] Microarray query   Umme Rummana
• [BioC] (no subject)   Umme Rummana
• [BioC] Microarray query   Umme Rummana
• [BioC] Retrieving a subset from normalized microarray data for differential test in R package, Limma   Arthur SHEN
• [BioC] Compatibility of Biorad cfx files to HTqPCR?   TP Sahoo
• [BioC] [Bioc-devel] Bioconductor 2.8 is released   Markus Schmidberger
• [BioC] prepare data matrix for siggenes   Holger Schwender
• [BioC] siggenes sam2excel Error   Holger Schwender
• [BioC] siggenes sam2excel Error   Holger Schwender
• [BioC] lmFit only deals with numerical values (data matrix object)?   Holger Schwender
• [BioC] Can't reproduce assessment data included in affycomp package   Philippe Serhal
• [BioC] RCytoscape error with deleteSelectedEdges   Paul Shannon
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   Wei Shi
• [BioC] Limma   Wei Shi
• [BioC] Limma   Wei Shi
• [BioC] summarized expression values from beadarray versus GenomeStudio   Wei Shi
• [BioC] avereps function in limma (dealing with negative values in illumina)   Wei Shi
• [BioC] avereps function in limma (dealing with negative values in illumina)   Wei Shi
• [BioC] LIMMA design question   Wei Shi
• [BioC] what to do with microarray outliers?   Wei Shi
• [BioC] what to do with microarray outliers?   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] multiple hits with countOverlaps function   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   Wei Shi
• [BioC] Rsubread alingner   Wei Shi
• [BioC] Rsubread alingner   Wei Shi
• [BioC] Rsubread alingner   Wei Shi
• [BioC] Rsubread alingner   Wei Shi
• [BioC] RNASeq: normalization issues   Wei Shi
• [BioC] RNASeq: normalization issues   Wei Shi
• [BioC] RNASeq: normalization issues   Wei Shi
• [BioC] RNASeq: normalization issues   Wei Shi
• [BioC] pdInfoBuilder   Barbara Shih
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Jason Shoemaker
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Jason Shoemaker
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Jason Shoemaker
• [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..   Jason Shoemaker
• [BioC] Integration   Prasad Siddavatam
• [BioC] limma complex contrast matrix   Prasad Siddavatam
• [BioC] avereps function in limma (dealing with negative values in illumina)   Prasad Siddavatam
• [BioC] avereps function in limma (dealing with negative values in illumina)   Prasad Siddavatam
• [BioC] LIMMA design question   Prasad Siddavatam
• [BioC] LIMMA design question   Prasad Siddavatam
• [BioC] beadarray: Running BASH for 120 sections   Mike Smith
• [BioC] beadarray: Running BASH for 120 sections   Mike Smith
• [BioC] beadarray: Running BASH for 120 sections   Mike Smith
• [BioC] edgeR - MDS plot   Gordon K Smyth
• [BioC] edgeR glm   Gordon K Smyth
• [BioC] edgeR glm   Gordon K Smyth
• [BioC] limma   Gordon K Smyth
• [BioC] limma   Gordon K Smyth
• [BioC] identifying consistently expressed genes between replicates   Gordon K Smyth
• [BioC] identifying consistently expressed genes between replicates   Gordon K Smyth
• [BioC] limma   Gordon K Smyth
• [BioC] identifying consistently expressed genes between replicates   Gordon K Smyth
• [BioC] warnings or potential problems in limma procedure   Gordon K Smyth
• [BioC] Paired tests using limma and beadarray   Gordon K Smyth
• [BioC] how to do paired t-tests for multiple subgroups [was: warnings or potential problems in limma procedure]   Gordon K Smyth
• [BioC] Paired tests using limma and beadarray   Gordon K Smyth
• [BioC] RNA-Seq with multiple factors [was Informations about DESeq package]   Gordon K Smyth
• [BioC] LIMMA: donor effect   Gordon K Smyth
• [BioC] Help on references for R Bioconductor   Srikanth Manda Srinivas
• [BioC] Help on references for R Bioconductor   Srikanth Manda Srinivas
• [BioC] Bioconductor 2.8 is released   Dan Tenenbaum
• [BioC] Biobase 2.8 with R 2.13.0 fails on my Mac   Dan Tenenbaum
• [BioC] arrayQualityMetrics with R 2.13.0 fails   Dan Tenenbaum
• [BioC] Biobase 2.8 with R 2.13.0 fails on my Mac   Dan Tenenbaum
• [BioC] [Bioc-devel] Bioconductor 2.8 is released   Dan Tenenbaum
• [BioC] [Bioc-sig-seq] Bioconductor 2.8 is released   Dan Tenenbaum
• [BioC] Biobase 2.8 with R 2.13.0 fails on my Mac   Dan Tenenbaum
• [BioC] BioC in the cloud (was Re: [Bioc-devel] Bioconductor 2.8 is released)   Dan Tenenbaum
• [BioC] Bioconductor AMI Amazon EC2 help   Dan Tenenbaum
• [BioC] problem installing affyPLMpackage   Dan Tenenbaum
• [BioC] Bioconductor AMI Amazon EC2 help   Dan Tenenbaum
• [BioC] arch=i386   Dan Tenenbaum
• [BioC] Creating 2 Gaussian Probability Density Function   Tim Triche, Jr.
• [BioC] strand-specificity for interval_overlap (girafe/genomeIntervals)   Joern Toedling
• [BioC] snp anotation   Fabrice Tourre
• [BioC] deseq for multiple groups with no replicate   Yolande Tra
• [BioC] deseq for multiple groups with no replicate   Yolande Tra
• [BioC] deseq for multiple groups with no replicate   Yolande Tra
• [BioC] deseq for multiple groups with no replicate   Yolande Tra
• [BioC] deseq for multiple groups with no replicate   Yolande Tra
• [BioC] removal of affymetrix control probes from ExpressionSet   Brian Tsai
• [BioC] How to get R plots with FastRweb   Simon Urbanek
• [BioC] R for normalizing gene length for next-gene sequencing data   Andrew Wang
• [BioC] gsea (gene set enrichment analysis) for ranked lists   Luo Weijun
• [BioC] advise normalization for Agilent one color Microarray for mRNA and miRNA   Anke Wendschlag
• [BioC] Normalizing together Nimblegen arrays with different designs   Wlasiuk Battagliotti, Gabriela - (wlasiuk)
• [BioC] Output IUPAC genotypes from oligo?   Hollis Wright
• [BioC] pa.calls-function in package "panp"   Samuel Wuest
• [BioC] merged affy 430 A&B   YBao
• [BioC] merged affy 430 A&B   YBao
• [BioC] GOstats problem with output   Assa Yeroslaviz
• [BioC] GOstats problem with output   Assa Yeroslaviz
• [BioC] conditional replace column values with values from a different column   Assa Yeroslaviz
• [BioC] image size - How to make bigger images   Assa Yeroslaviz
• [BioC] image size - How to make bigger images   Assa Yeroslaviz
• [BioC] drosophila2cdf.qcdf   Assa Yeroslaviz
• [BioC] simpleafy plots   Assa Yeroslaviz
• [BioC] warnings or potential problems in limma procedure   Yi, Ming (NIH/NCI) [C]
• [BioC] warnings or potential problems in limma procedure   Yi, Ming (NIH/NCI) [C]
• [BioC] warnings or potential problems in limma procedure   Yi, Ming (NIH/NCI) [C]
• [BioC] how to do paired t-tests for multiple subgroups [was: warnings or potential problems in limma procedure]   Yi, Ming (NIH/NCI) [C]
• [BioC] Biobase 2.8 with R 2.13.0 fails on my Mac   Janet Young
• [BioC] rtracklayer gff import   Kathi Zarnack
• [BioC] Regarding the ChIPpeakAnno Package   Zhu, Lihua (Julie)
• [BioC] Using ChIPpeakAnno on a non-mainstream organism   Zhu, Lihua (Julie)
• [BioC] Draw histogram with an optional "Weight" column   Zhu, Lihua (Julie)
• [BioC] advise normalization for Agilent one color Microarray for mRNA and miRNA   axel.klenk at actelion.com
• [BioC] Read.maimages with Mac OS X v.10.6 Snow Leopard - SessionInfo update   axel.klenk at actelion.com
• [BioC] LIMMA: donor effect   somnath bandyopadhyay
• [BioC] LIMMA: donor effect   somnath bandyopadhyay
• [BioC] gff files: how to tell if right-open interval convention used?   karlerhard at berkeley.edu
• [BioC] girafe issues - no interval overlap   karlerhard at berkeley.edu
• [BioC] strand-specificity for interval_overlap (girafe/genomeIntervals)   karlerhard at berkeley.edu
• [BioC] Converting list to a matrix   pankaj borah
• [BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?   nqueralt at clinic.ub.es
• [BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?   cstrato
• [BioC] XPS: new quality control features (e.g. residual images)   cstrato
• [BioC] two questions regarding Human Gene 1.0 ST arrays   cstrato
• [BioC] two questions regarding Human Gene 1.0 ST arrays   cstrato
• [BioC] two questions regarding Human Gene 1.0 ST arrays   cstrato
• [BioC] Human Gene array data analysis workflow   cstrato
• [BioC] Human Gene array data analysis workflow   cstrato
• [BioC] Eleonore Gravier/CURIE est absent(e).   eleonore.gravier at curie.net
• [BioC] question about topTable in limma   samane fazeli
• [BioC] Combining data from different versions of Illumina HumanHT-12 v3   gavin.koh at gmail.com
• [BioC] M values; and dist functions   john herbert
• [BioC] [Course] CSAMA 2011: Computational Statistics for Genome Biology (Ninth Edition)   stefano iacus
• [BioC] prepare data matrix for siggenes   joseph
• [BioC] prepare data matrix for siggenes   joseph
• [BioC] siggenes sam2excel Error   joseph
• [BioC] siggenes sam2excel Error   joseph
• [BioC] Creating 2 Gaussian Probability Density Function   viritha kaza
• [BioC] Limma creating model.matrix   viritha kaza
• [BioC] Limma creating model.matrix   viritha kaza
• [BioC] qvalue package:pFDR generation from pvalues   viritha kaza
• [BioC] Creating 2 Gaussian Probability Density Function   viritha kaza
• [BioC] Microarray query   viritha kaza
• [BioC] Microarray query   viritha kaza
• [BioC] Microarray query   viritha kaza
• [BioC] karyotype annotation   J.Oosting at lumc.nl
• [BioC] karyotype annotation   J.Oosting at lumc.nl
• [BioC] GoStats and microRNA pipeline using Biomart   David martin
• [BioC] LDA and qPCR data   David martin
• [BioC] problem with biomaRt package using mart "snps", dataset "hsapiens_structvar", attribute "description"   mmaguire
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   adeonari at mrc-lmb.cam.ac.uk
• [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis   adeonari at mrc-lmb.cam.ac.uk
• [BioC] ENVISIONQuery package   yotsawat pomyen
• [BioC] ENVISIONQuery package   yotsawat pomyen
• [BioC] system() command in R   rasanpreet kaur suri
• [BioC] EBarrays question   jgomez at uni-potsdam.de
• [BioC] EBarrays question   jgomez at uni-potsdam.de
• [BioC] inconsistency between GRangesList and transcriptDB object.   zhenjiang xu

Last message date: Sat Apr 30 12:53:12 CEST 2011
Archived on: Sat Apr 30 12:53:58 CEST 2011

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