October 2011 Archives by author

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Starting: Sat Oct 1 00:11:00 CEST 2011
Ending: Mon Oct 31 22:15:26 CET 2011
Messages: 467

• [BioC] GEOquery, Limma Annotations   Ovokeraye Achinike-Oduaran
• [BioC] GEOquery, Limma Annotations   Ovokeraye Achinike-Oduaran
• [BioC] GEO and Limma   Ovokeraye Achinike-Oduaran
• [BioC] GEO and Limma   Ovokeraye Achinike-Oduaran
• [BioC] GEO and Limma   Ovokeraye Achinike-Oduaran
• [BioC] postForm in RCurl   Ovokeraye Achinike-Oduaran
• [BioC] postForm in RCurl   Ovokeraye Achinike-Oduaran
• [BioC] postForm in RCurl   Ovokeraye Achinike-Oduaran
• [BioC] Limma and Names Assignment   Ovokeraye Achinike-Oduaran
• [BioC] Limma and Names Assignment   Ovokeraye Achinike-Oduaran
• [BioC] PostForm and readHTML Table   Ovokeraye Achinike-Oduaran
• [BioC] GEOquery and Limma   Ovokeraye Achinike-Oduaran
• [BioC] Faculty position at Penn State (Bioinformatics and/or Statistics)   Naomi Altman
• [BioC] heatmap.2 Z-score vs logFC   Neel Aluru
• [BioC] heatmap.2 Z-score vs logFC   Neel Aluru
• [BioC] uneven counts for edgeR   Simon Anders
• [BioC] control probes and missing annotations in Affy Mouse Gene 1.0 ST arrays   Jeroen BOGIE
• [BioC] Reading paired-end data into GRangesList   Cory Barr
• [BioC] Reading paired-end data into GRangesList   Cory Barr
• [BioC] Illumina array analysis   Belmont, John W
• [BioC] PICS   Arnaud BioC
• [BioC] Agi4x44PreProcess package: Error in build.est   Jarek Bryk
• [BioC] best annotation package for drosophila (agilent gene expression)?   Jarek Bryk
• [BioC] Agi4x44Preprocess/Limma and number of significant p-values   Jarek Bryk
• [BioC] course announcement: Bioconductor basics, 24-25 oct 2011, Longwood Medical Area, Boston   Vincent Carey
• [BioC] need help with SNP6.0 quantile normalization   Vincent Carey
• [BioC] Boston Bioconductor Basics registration will close tomorrow.   Vincent Carey
• [BioC] GRanges findOverlaps error   Vincent Carey
• [BioC] ShortRead::report() breaks in mac osx   Vincent Carey
• [BioC] silly looping question   Benilton Carvalho
• [BioC] rma of oligo feature set crashes R   Benilton Carvalho
• [BioC] need help with SNP6.0 quantile normalization   Benilton Carvalho
• [BioC] need help with SNP6.0 quantile normalization_How to extract reference distribution   Benilton Carvalho
• [BioC] SNP 6 chip   Benilton Carvalho
• [BioC] Erros in crlmm Re: SNP 6 chip   Benilton Carvalho
• [BioC] Erros in crlmm Re: SNP 6 chip   Benilton Carvalho
• [BioC] Ensembl websites offline for maintenance   Robert Castelo
• [BioC] ShortRead::report() breaks in mac osx   Robert Castelo
• [BioC] ShortRead::report() breaks in mac osx   Robert Castelo
• [BioC] reducing hits from countGenomicOverlaps()   Robert Castelo
• [BioC] reducing hits from countGenomicOverlaps()   Robert Castelo
• [BioC] reducing hits from countGenomicOverlaps()   Robert Castelo
• [BioC] Bioinformatics course - October 2011 Registration is now open   Claude Chelala
• [BioC] Illumina array analysis   Chintanu
• [BioC] Illumina array analysis   Chintanu
• [BioC] Illumina array analysis   Chintanu
• [BioC] Illumina array analysis   Chintanu
• [BioC] R/Bioconductor package to analyze illumina iscan genotyping data   John Clark
• [BioC] silly looping question   Nathalie Conte
• [BioC] "internal equal" overlap mode for GRangesList   Cook, Malcolm
• [BioC] Regression analysis problem   Kevin R. Coombes
• [BioC] Importing .cdt files generated by Cluster3.0 into R   Kevin R. Coombes
• [BioC] removeBatchEffect problem   John Coulthard
• [BioC] removeBatchEffect problem   John Coulthard
• [BioC] removeBatchEffect problem   John Coulthard
• [BioC] illuminaHumanv4 mappings   Mark Cowley
• [BioC] two way ANOVA with limma   Grant R Cramer
• [BioC] GEOquery returns error "scan() expected 'an integer'"   Sean Davis
• [BioC] GEOquery returns error "scan() expected 'an integer'"   Sean Davis
• [BioC] GEO and Limma   Sean Davis
• [BioC] RankProd related question   Sean Davis
• [BioC] Regression analysis problem   Sean Davis
• [BioC] mapping through org.Xx.eg.db packages   Sean Davis
• [BioC] the same problem happened   Sean Davis
• [BioC] how to update a bioconductor package   Sean Davis
• [BioC] the same problem happened   Sean Davis
• [BioC] how to update a bioconductor package   Sean Davis
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Sean Davis
• [BioC] [Job] Functional genomic analysis of cancer/RNAi screening   Sean Davis
• [BioC] Problem with a specific GEO dataset.   Sean Davis
• [BioC] Limma and Names Assignment   Sean Davis
• [BioC] GEOquery and Limma   Sean Davis
• [BioC] heatmap.2 Z-score vs logFC   Sean Davis
• [BioC] DNase Seq Analysis using R   Sean Davis
• [BioC] miRNA 2.0 Array, Annotation Files how to use it after rma and readaffy   Sean Davis
• [BioC] annotation file and expression set genechip miRNA 2 array   Sean Davis
• [BioC] breastCancerNKI patients question   Sean Davis
• [BioC] any package to do gene expression value estimation   Sean Davis
• [BioC] "internal equal" overlap mode for GRangesList   Sean Davis
• [BioC] error with MEDIPS.CpGenrich when using extend   Joern Dietrich
• [BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?   Ian Donaldson
• [BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?   Ian Donaldson
• [BioC] annotation package for Schizosacharomyces pombe   Clémentine Dressaire
• [BioC] PICS   Arnaud Droit
• [BioC] Merge dataframes   "João Daniel N. Duarte"
• [BioC] Merge dataframes   João Daniel Nunes Duarte
• [BioC] [BioMart Users] biomaRt returning multiple columns out of order   Steffen Durinck
• [BioC] Manual creation of Affybatch object to study highthrouput qPCR experiments.   Heidi Dvinge
• [BioC] perWindow chr coordinates (girafe)   Karl Erhard
• [BioC] [flowCore] problems with read.flowSet   Finak, Greg
• [BioC] Statistical programmer position at FHCRC   Finak, Greg
• [BioC] GEOquery returns error "scan() expected 'an integer'"   Timothée Flutre
• [BioC] GEOquery returns error "scan() expected 'an integer'"   Timothée Flutre
• [BioC] GEO and Limma   Freudenberg, Johannes (NIH/NIEHS) [E]
• [BioC] NUSE and RLE PLOTS for ST1.0 Gene chips with oligo w/o 1st quantile line   Richard Friedman
• [BioC] Practical utilization of SQN in ST1.0 Gene normalization.   Richard Friedman
• [BioC] Practical utilization of SQN in ST1.0 Gene normalization.   Richard Friedman
• [BioC] [flowCore] problems with read.flowSet   Stephan Fuhrmann
• [BioC] mapping through org.Xx.eg.db packages   Iain Gallagher
• [BioC] visualise model fit in edgeR   Iain Gallagher
• [BioC] visualise model fit in edgeR   Iain Gallagher
• [BioC] Problem with tkWidgets   Ignacio Lopez De Ullibarri Galparsoro
• [BioC] Creating One Single Object with Phenotype and Expression Data   Ben Ganzfried
• [BioC] Fwd: Creating One Single Object with Phenotype and Expression Data   Ben Ganzfried
• [BioC] [BioMart Users] biomaRt returning multiple columns out of order   Laurent Gatto
• [BioC] poe.mcmc - phenotypic label - coding   Debashis Ghosh
• [BioC] Analysis of Affymetrix Cytogenetic Whole-Genome 2.7M array   Lavinia Gordon
• [BioC] annotation db for miRNA_2 Array   Jan Van der Goten
• [BioC] Chip-seq quality control   Ivan Gregoretti
• [BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?   Ivan Gregoretti
• [BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?   Ivan Gregoretti
• [BioC] how to extract promoter regions and detect motif occurrence counts?   Ivan Gregoretti
• [BioC] Overlap of 3 gene lists and the Mantel-Haenszel test   Edwin Groot
• [BioC] breastCancerNKI patients question   Benjamin Haibe-Kains
• [BioC] rma of oligo feature set crashes R   Thomas H. Hampton
• [BioC] heat map for a time course study   Thomas H. Hampton
• [BioC] unable to install lumi package   Juliet Hannah
• [BioC] present / absent calls and detection p-values   Kasper Daniel Hansen
• [BioC] how to update a bioconductor package   Kasper Daniel Hansen
• [BioC] Installing packages on R v2.13.2, OSX multiple warning messages   Kasper Daniel Hansen
• [BioC] Identifying the genome sequence of an affy probe   Kasper Daniel Hansen
• [BioC] how to extract promoter regions and detect motif occurrence counts?   Yuan Hao
• [BioC] [BioMart Users] biomaRt returning multiple columns out of order   Richard Hayes
• [BioC] present / absent calls and detection p-values   Andreas Heider
• [BioC] [question] integration of microarray data from different sources in limma package   Andreas Heider
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Emanuel Heitlinger
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Emanuel Heitlinger
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Emanuel Heitlinger
• [BioC] R/Bioconductor CDF to Affymetrix CDF   Hooiveld, Guido
• [BioC] CDF for GeneChip miRNA 2 array   Hooiveld, Guido
• [BioC] about refseq_dna in biomat   Hans-Rudolf Hotz
• [BioC] Binomial regression of HTqPCR data   Christopher Howerton
• [BioC] Conference announcement: Omics and Personalised Health, EMBL Heidelberg, 16-18 February 2012   Wolfgang Huber
• [BioC] Fwd: Creating One Single Object with Phenotype and Expression Data   Wolfgang Huber
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Wolfgang Huber
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Wolfgang Huber
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Wolfgang Huber
• [BioC] biomaRt query problems- plants_mart_10   Wolfgang Huber
• [BioC] Error loading library   Wolfgang Huber
• [BioC] Bioconductor Digest, Vol 104, Issue 7   Stefan McKinnon Høj-Edwards
• [BioC] still the trimLRPatterns problem   Harris A. Jaffee
• [BioC] report a problem (trimLRPatterns not symmetric?)   Harris A. Jaffee
• [BioC] Error loading library   Nurdiyanah Jambari
• [BioC] [flowCore] problems with read.flowSet   Jiang, Mike
• [BioC] Ensembl websites offline for maintenance   Rhoda Kinsella
• [BioC] Ensembl websites offline for maintenance   Rhoda Kinsella
• [BioC] Ensembl websites offline for maintenance   Rhoda Kinsella
• [BioC] Connecting to Uniprot Biomart using biomaRt   Rhoda Kinsella
• [BioC] Connecting to Uniprot Biomart using biomaRt   Rhoda Kinsella
• [BioC] biomaRt query ??   Rhoda Kinsella
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Duncan Temple Lang
• [BioC] postForm in RCurl   Duncan Temple Lang
• [BioC] [Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values   Michael Lawrence
• [BioC] Coverage by base   Michael Lawrence
• [BioC] Coverage by base   Michael Lawrence
• [BioC] Coverage of reads in 3'UTR   Michael Lawrence
• [BioC] GRanges findOverlaps error   Michael Lawrence
• [BioC] biocLite breaks when `svn rev` is "unknown"   Michael Lawrence
• [BioC] extending XString to facilitate miRNA editing   Michael Lawrence
• [BioC] biocLite breaks when `svn rev` is "unknown"   Michael Lawrence
• [BioC] "internal equal" overlap mode for GRangesList   Michael Lawrence
• [BioC] extending XString to facilitate miRNA editing   Jeremy Leipzig
• [BioC] Reading paired-end data into GRangesList   Paul Leo
• [BioC] how to deal with a 30G fastq file   Steve Lianoglou
• [BioC] how to deal with Fastq file more than 30G   Steve Lianoglou
• [BioC] Coverage by base   Steve Lianoglou
• [BioC] Coverage by base   Steve Lianoglou
• [BioC] Coverage by base   Steve Lianoglou
• [BioC] how to extract promoter regions and detect motif occurrence counts?   Steve Lianoglou
• [BioC] Identifying the genome sequence of an affy probe   Steve Lianoglou
• [BioC] goSeq error   Steve Lianoglou
• [BioC] Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser   Jason Lu
• [BioC] Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser   Jason Lu
• [BioC] any package to do gene expression value estimation   Jason Lu
• [BioC] Problem with tkWidgets   James W. MacDonald
• [BioC] Regression analysis problem   James W. MacDonald
• [BioC] Installing packages on R v2.13.2, OSX multiple warning messages   James W. MacDonald
• [BioC] a question about getCdfInfo package in GCRMA, thanks for your help.   James W. MacDonald
• [BioC] Limma model parameters design, combining a paired with a factorial design   James W. MacDonald
• [BioC] question about affymetrix array:ht-hg-u133acdf   James W. MacDonald
• [BioC] R/Bioconductor CDF to Affymetrix CDF   James W. MacDonald
• [BioC] \'mirna20probe   James W. MacDonald
• [BioC] SNP 6 chip   James W. MacDonald
• [BioC] Manual creation of Affybatch object to study highthrouput qPCR experiments.   James W. MacDonald
• [BioC] removeBatchEffect problem   James W. MacDonald
• [BioC] removeBatchEffect problem   James W. MacDonald
• [BioC] Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser   James W. MacDonald
• [BioC] Probe Coordinates for the Affymetrix U133 2.0 plus array in the UCSC genome browser   James W. MacDonald
• [BioC] F values from topTable with coef=NULL testing all zero or all equal?   James W. MacDonald
• [BioC] Identifying the genome sequence of an affy probe   James W. MacDonald
• [BioC] unable to install lumi package   James W. MacDonald
• [BioC] (BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem   Elisabetta Manduchi
• [BioC] (BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem   Elisabetta Manduchi
• [BioC] error with MEDIPS.CpGenrich when using extend   Elisabetta Manduchi
• [BioC] limma suitability for correlated data   Max Mariasegaram
• [BioC] heatmap.2 function and the scale option   Aleš Maver
• [BioC] Merge dataframes   Aleš Maver
• [BioC] problem with frma( )   Matthew McCall
• [BioC] Postdoctoral position in biostatistics/bioinformatics/computational biology   Medvedovic, Mario (medvedm)
• [BioC] Computational biologist positions at the PICR   Crispin Miller
• [BioC] Agi4x44PreProcess package: Error in build.est   Jon Mohl
• [BioC] Agi4x44PreProcess package: Error in build.est   Jon Mohl
• [BioC] Chip-seq quality control   Martin Morgan
• [BioC] how to deal with a 30G fastq file   Martin Morgan
• [BioC] mapping through org.Xx.eg.db packages   Martin Morgan
• [BioC] 'parallel' vs 'multicore'   Martin Morgan
• [BioC] how to deal with a 30G fastq file   Martin Morgan
• [BioC] 'parallel' vs 'multicore'   Martin Morgan
• [BioC] Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)   Martin Morgan
• [BioC] Is it possible to generate an ExpressionSet object that contain duplicate row names?   Martin Morgan
• [BioC] ArrayExpressHTS fails to load   Martin Morgan
• [BioC] biocLite breaks when `svn rev` is "unknown"   Martin Morgan
• [BioC] CLLbatch does not work   Martin Morgan
• [BioC] biocLite breaks when `svn rev` is "unknown"   Martin Morgan
• [BioC] any package to do gene expression value estimation   Martin Morgan
• [BioC] comparing two tables   Martin Morgan
• [BioC] any package to do gene expression value estimation   Martin Morgan
• [BioC] any package to do gene expression value estimation   Martin Morgan
• [BioC] reducing hits from countGenomicOverlaps()   Martin Morgan
• [BioC] PostForm and readHTML Table   Martin Morgan
• [BioC] Reading paired-end data into GRangesList   Martin Morgan
• [BioC] F values from topTable with coef=NULL testing all zero or all equal?   Michael Muratet
• [BioC] Fwd: F values from topTable with coef=NULL testing all zero or all equal?   Michael Muratet
• [BioC] F values from topTable with coef=NULL testing all zero or all equal?   Michael Muratet
• [BioC] Single channel microarray   Niraj Nepal
• [BioC] Agi4x44Preprocess/Limma and number of significant p-values   Paulo Nuin
• [BioC] Rsamtools question   Valerie Obenchain
• [BioC] Rsamtools question   Valerie Obenchain
• [BioC] Importing .cdt files generated by Cluster3.0 into R   Valerie Obenchain
• [BioC] reducing hits from countGenomicOverlaps()   Valerie Obenchain
• [BioC] reducing hits from countGenomicOverlaps()   Valerie Obenchain
• [BioC] heatmap.2 Z-score vs logFC   Ochsner, Scott A
• [BioC] R/Bioconductor CDF to Affymetrix CDF   Benjamin Otto
• [BioC] R/Bioconductor CDF to Affymetrix CDF   Benjamin Otto
• [BioC] about refseq_dna in biomat   Ou, Jianhong
• [BioC] about refseq_dna in biomat   Ou, Jianhong
• [BioC] [Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values   Hervé Pagès
• [BioC] how to update a bioconductor package   Hervé Pagès
• [BioC] how to update a bioconductor package   Hervé Pagès
• [BioC] (BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem   Hervé Pagès
• [BioC] Coverage by base   Hervé Pagès
• [BioC] Coverage by base   Hervé Pagès
• [BioC] edgeR on microRNA data   Hervé Pagès
• [BioC] rma of oligo feature set crashes R   Hervé Pagès
• [BioC] Coverage by base   Hervé Pagès
• [BioC] BSgenome package for sacCer3   Hervé Pagès
• [BioC] Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors   Kurinji Pandiyan
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Paniagua, Eric
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Paniagua, Eric
• [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?   Paniagua, Eric
• [BioC] Chip-seq quality control   Lucia Peixoto
• [BioC] Chip-seq quality control   Lucia Peixoto
• [BioC] Agi4x44PreProcess package: Error in build.est   Francois Pepin
• [BioC] Agi4x44PreProcess package: Error in build.est   Francois Pepin
• [BioC] Manual creation of Affybatch object to study highthrouput qPCR experiments.   James Perkins
• [BioC] edgeR on microRNA data   Helena Persson
• [BioC] edgeR on microRNA data   Helena Persson
• [BioC] edgeR on microRNA data   Helena Persson
• [BioC] edgeR on microRNA data   Helena Persson
• [BioC] Comparing two gff/gtf files : de novo transcripts v/s reference   Abhishek Pratap
• [BioC] RankProd related question   Wendy Qiao
• [BioC] find unregulated genes from ranks   Wendy Qiao
• [BioC] Rsamtools question   Alpesh Querer
• [BioC] Reading paired-end data into GRangesList   Hubert Rehrauer
• [BioC] Reading paired-end data into GRangesList   Hubert Rehrauer
• [BioC] Reading paired-end data into GRangesList   Hubert Rehrauer
• [BioC] breastCancerNKI patients question   Xavier Robin
• [BioC] breastCancerNKI patients question   Xavier Robin
• [BioC] breastCancerNKI patients question   Xavier Robin
• [BioC] Postdoctoral Position in Statistical Genomics - Zurich   Mark Robinson
• [BioC] edgeR design matrix   Mark Robinson
• [BioC] edgeR: plotSmear for multiple detags   Mark Robinson
• [BioC] ArrayExpressHTS fails to load   Sean Rogers
• [BioC] DNase Seq Analysis using R   Samarjeet
• [BioC] SNP 6 chip   Samarjeet
• [BioC] RNA-Seq : comparison cuffdiff, edgeR, Partek   Lana Schaffer
• [BioC] uneven counts for edgeR   Lana Schaffer
• [BioC] PCR bias in RNA-Seq   Lana Schaffer
• [BioC] uneven counts for edgeR   Lana Schaffer
• [BioC] RNA-Seq: lognormal, Neg Bin, Poisson distribution   Lana Schaffer
• [BioC] uneven counts for edgeR   Lana Schaffer
• [BioC] breastCancerNKI patients question   Markus Schroeder
• [BioC] Merge dataframes   D. Schruth
• [BioC] Problems with edgeR for differential expression.   Nick Schurch
• [BioC] Problems with edgeR for differential expression   Nick Schurch
• [BioC] Fwd: Problems with edgeR for differential expression   Nick Schurch
• [BioC] Problems with edgeR for differential expression   Nick Schurch
• [BioC] Identifying the genome sequence of an affy probe   Schragi Schwartz
• [BioC] Identifying the genome sequence of an affy probe   Schragi Schwartz
• [BioC] edgeR: plotSmear for multiple detags   steve Shen
• [BioC] edgeR: plotSmear for multiple detags   steve Shen
• [BioC] edgeR: plotSmear for multiple detags   steve Shen
• [BioC] goSeq error   steve Shen
• [BioC] goSeq error   steve Shen
• [BioC] present / absent calls and detection p-values   Wei Shi
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Wei Shi
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Wei Shi
• [BioC] Regarding subread vignette   Wei Shi
• [BioC] Regarding subread vignette   Wei Shi
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Wei Shi
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Wei Shi
• [BioC] Illumina array analysis   Wei Shi
• [BioC] Illumina array analysis   Wei Shi
• [BioC] Illumina array analysis   Wei Shi
• [BioC] Illumina array analysis   Wei Shi
• [BioC] Illumina array analysis   Wei Shi
• [BioC] any package to do gene expression value estimation   Wei Shi
• [BioC] any package to do gene expression value estimation   Wei Shi
• [BioC] topGO graph visualization functions crashing under R 2.13.2 with Graphviz 2.20.3.1   Joseph Skaf
• [BioC] biomaRt query ??   Tim Smith
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] edgeR on microRNA data   Gordon K Smyth
• [BioC] Problems with edgeR for differential expression   Gordon K Smyth
• [BioC] EdgeR: Log FC does not changes when I swap the groups   Gordon K Smyth
• [BioC] Problems with edgeR for differential expression   Gordon K Smyth
• [BioC] edgeR design matrix   Gordon K Smyth
• [BioC] Problems with edgeR for differential expression   Gordon K Smyth
• [BioC] two way ANOVA with limma   Gordon K Smyth
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Gordon K Smyth
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Gordon K Smyth
• [BioC] edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE   Gordon K Smyth
• [BioC] uneven counts for edgeR   Gordon K Smyth
• [BioC] uneven counts for edgeR   Gordon K Smyth
• [BioC] visualise model fit in edgeR   Gordon K Smyth
• [BioC] limma printer layout   Gordon K Smyth
• [BioC] Mapping deletions onto chromosome ideograms   Srinivas Srikanth
• [BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?   Rory Stark
• [BioC] edgeR on microRNA data   Dan Tenenbaum
• [BioC] ArrayExpressHTS fails to load   Dan Tenenbaum
• [BioC] biomaRt query problems- plants_mart_10   Dan Tenenbaum
• [BioC] Connecting to Uniprot Biomart using biomaRt   Dan Tenenbaum
• [BioC] Fwd: Connecting to Uniprot Biomart using biomaRt   Dan Tenenbaum
• [BioC] Error loading library   Dan Tenenbaum
• [BioC] Error loading library   Dan Tenenbaum
• [BioC] unable to install lumi package   Dan Tenenbaum
• [BioC] Regression analysis problem   Andrew Teschendorff
• [BioC] 'parallel' vs 'multicore'   Tim Triche, Jr.
• [BioC] 'parallel' vs 'multicore'   Tim Triche, Jr.
• [BioC] Regression analysis problem   Tim Triche, Jr.
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Tim Triche, Jr.
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Tim Triche, Jr.
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Tim Triche, Jr.
• [BioC] Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)   Tim Triche, Jr.
• [BioC] Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)   Tim Triche, Jr.
• [BioC] Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts   Tim Triche, Jr.
• [BioC] Is it possible to generate an ExpressionSet object that contain duplicate row names?   Tim Triche, Jr.
• [BioC] liftOver() issues   Tim Triche, Jr.
• [BioC] Illumina array analysis   Tim Triche, Jr.
• [BioC] Practical utilization of SQN in ST1.0 Gene normalization.   Tim Triche, Jr.
• [BioC] Practical utilization of SQN in ST1.0 Gene normalization.   Tim Triche, Jr.
• [BioC] perWindow chr coordinates (girafe)   Joern Toedling
• [BioC] how to extract promoter regions and detect motif occurrence counts?   Edward Turner
• [BioC] Problem with limma for two-color factorial design - Coefficients not estimable   Stephen Turner
• [BioC] Regression analysis using expression microarray to determine phenotypic correlation   Ruppert Valentino
• [BioC] problem with frma( )   Wang,Ying
• [BioC] limma data frame subsetting problem   Jabez Wilson
• [BioC] limma data frame subsetting problem   Jabez Wilson
• [BioC] [R] comparing two tables   David Winsemius
• [BioC] R/Bioconductor CDF to Affymetrix CDF   Samuel Wuest
• [BioC] biomaRt query problems- plants_mart_10   Samuel Wuest
• [BioC] biomaRt query problems- plants_mart_10   Samuel Wuest
• [BioC] comparing two tables   Assa Yeroslaviz
• [BioC] comparing two tables   Assa Yeroslaviz
• [BioC] Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?   Peng Yu
• [BioC] GRanges findOverlaps error   Kathi Zarnack
• [BioC] GetEnrichedGo term   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno - for genes with multiple isoforms   Zhu, Lihua (Julie)
• [BioC] PICS   Zhu, Lihua (Julie)
• [BioC] PICS   Zhu, Lihua (Julie)
• [BioC] PICS   Zhu, Lihua (Julie)
• [BioC] PICS : makeRangedDataOutput   Zhu, Lihua (Julie)
• [BioC] CDF for GeneChip miRNA 2 array   ATTIA [guest]
• [BioC] feature filter for GENE Chip miRNA 2.0 array   ATTIA [guest]
• [BioC] \'mirna20probe   ATTIA [guest]
• [BioC] Manual creation of Affybatch object to study highthrouput qPCR experiments.   Ali Mo [guest]
• [BioC] annotation dbi for miRNA 2.0 Array   Attia [guest]
• [BioC] miRNA 2.0 Array, Annotation Files how to use it after rma and readaffy   Attia [guest]
• [BioC] annotation file and expression set genechip miRNA 2 array   Attia [guest]
• [BioC] Error with read.SMD() of marray   Ignacio Lopez de Ullibarri [guest]
• [BioC] Problem with tkWidgets   Ignacio López de Ullibarri [guest]
• [BioC] read.maimage error message   Kathy [guest]
• [BioC] question about affymetrix array:ht-hg-u133acdf   Richard [guest]
• [BioC] Pie chart   Roopa Subbaiah [guest]
• [BioC] Installing packages on R v2.13.2, OSX multiple warning messages   Sarah Little [guest]
• [BioC] Problem with a specific GEO dataset.   Shawn Garbett [guest]
• [BioC] Importing .cdt files generated by Cluster3.0 into R   Sohail [guest]
• [BioC] Error loading library   diyanah [guest]
• [BioC] EdgeR: Log FC does not changes when I swap the groups   saad khan [guest]
• [BioC] CLLbatch does not work   william [guest]
• [BioC] limma data frame subsetting problem   axel.klenk at actelion.com
• [BioC] limma data frame subsetting problem   axel.klenk at actelion.com
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage by base   rohan bareja
• [BioC] Coverage of reads in 3'UTR   rohan bareja
• [BioC] Coverage of reads in 3'UTR   rohan bareja
• [BioC] Normalization in Coverage   rohan bareja
• [BioC] makeContrasts function   konika chawla
• [BioC] Is it possible to generate an ExpressionSet object that contain duplicate row names?   nqueralt at clinic.ub.es
• [BioC] SNP 6 chip   cstrato
• [BioC] Connecting to Uniprot Biomart using biomaRt   kenny daily
• [BioC] annotation db for miRNA_2 Array   attia fatima
• [BioC] heatmap.2 function and the scale option   john herbert
• [BioC] heatmap.2 function and the scale option   john herbert
• [BioC] Limma model parameters design, combining a paired with a factorial design   john herbert
• [BioC] Limma model parameters design, combining a paired with a factorial design   john herbert
• [BioC] heat map for a time course study   blockaa at huskers.unl.edu
• [BioC] Regression analysis problem   khadeeja ismail
• [BioC] Regression analysis problem   khadeeja ismail
• [BioC] Regression analysis problem   khadeeja ismail
• [BioC] Regression analysis problem   khadeeja ismail
• [BioC] Regression analysis problem   khadeeja ismail
• [BioC] cghMCR package:Is it possible to find MCR by not usingDNAcopy object?   viritha k
• [BioC] SGOL plot   viritha k
• [BioC] SNP 6 chip   John linux-user
• [BioC] Erros in crlmm Re: SNP 6 chip   John linux-user
• [BioC] Erros in crlmm Re: SNP 6 chip   John linux-user
• [BioC] need help with SNP6.0 quantile normalization   qian liu
• [BioC] need help with SNP6.0 quantile normalization_How to extract reference distribution   qian liu
• [BioC] error in reading cel file for snp6.0 using aroma.affymetrix   qian liu
• [BioC] edgeR design matrix   lpascual
• [BioC] edgeR design matrix   lpascual
• [BioC] edgeR design matrix   lpascual
• [BioC] Help with comparisons of lists of fold changes   David martin
• [BioC] poe.mcmc - phenotypic label - coding   mjonczyk
• [BioC] poe.mcmc - phenotypic label - coding   mjonczyk
• [BioC] read.maimage error message   mjonczyk
• [BioC] a question about getCdfInfo package in GCRMA, thanks for your help.   mjonczyk
• [BioC] limma printer layout   mjonczyk
• [BioC] Help strange GSEA error   musa
• [BioC] Computational Biologist position available in Screening Unit in Milan, Italy   mattia pelizzola
• [BioC] how to deal with Fastq file more than 30G   wang peter
• [BioC] how to apply for a member in bioconductor maillist   wang peter
• [BioC] how to deal with a 30G fastq file   wang peter
• [BioC] the same problem happened   wang peter
• [BioC] how to update a bioconductor package   wang peter
• [BioC] still the trimLRPatterns problem   wang peter
• [BioC] report a problem   wang peter
• [BioC] how to define a forward or reverse read file   wang peter
• [BioC] how to check paired end data   wang peter
• [BioC] any package to do gene expression value estimation   wang peter
• [BioC] any package to do gene expression value estimation   wang peter
• [BioC] any package to do gene expression value estimation   wang peter
• [BioC] any package to do gene expression value estimation   wang peter
• [BioC] RNA-Seq : comparison cuffdiff, edgeR, Partek   vasu punj
• [BioC] DNase Seq Analysis using R   vasu punj
• [BioC] [BioMart Users] biomaRt returning multiple columns out of order   vasu punj
• [BioC] Illumina array analysis   vasu punj
• [BioC] Illumina array analysis   vasu punj
• [BioC] edgeR questions   Asma rabe
• [BioC] Fwd: edgeR questions   Asma rabe
• [BioC] Sample Grouping   rajasereddy
• [BioC] (no subject)   Jiuzhou song
• [BioC] edge R data reading   kuntal worah
• [BioC] a question about getCdfInfo package in GCRMA, thanks for your help.   liuyang zhao
• [BioC] [question] integration of microarray data from different sources in limma package   이선재
• [BioC] What is the difference of layout between genepix scanner & agilent scanner   이선재

Last message date: Mon Oct 31 22:15:26 CET 2011
Archived on: Tue Nov 1 00:39:14 CET 2011

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