July 2008 Archives by author

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Starting: Tue Jul 1 00:13:04 CEST 2008
Ending: Thu Jul 31 22:47:27 CEST 2008
Messages: 546

• [BioC] RMySQL   alex lam (RI)
• [BioC] Differences in readExpressionSet between R2.7.1 and R2.5.1 version   daphne mouzaki (RI)
• [BioC] cant install Rgraphviz   Vincent Carey 525-2265
• [BioC] hcluster crashes R environment   Vincent Carey 525-2265
• [BioC] LoadLibrary failures when loading RMySQL and xps packages   Vincent Carey 525-2265
• [BioC] Affymetrix probeset ids to gene symbols   Vincent Carey 525-2265
• [BioC] smlSet and snpMatrix / copy number analysis   Vincent Carey 525-2265
• [BioC] Question about 'annFUN.db' in topGO ....   ALok
• [BioC] GEOquery::parseGEO throws error reading file   Gad Abraham
• [BioC] GEOquery   Cei Abreu-Goodger
• [BioC] GEOquery   Cei Abreu-Goodger
• [BioC] SQLForge and probes that map to multiple genes   Cei Abreu-Goodger
• [BioC] SQLForge and probes that map to multiple genes   Cei Abreu-Goodger
• [BioC] SQLForge and probes that map to multiple genes   Cei Abreu-Goodger
• [BioC] Howto Get GO/Gene-names of GEO-Soft Probe-names   Cei Abreu-Goodger
• [BioC] LoadLibrary failures when loading RMySQL and xps packages   Marie Chehani Alles
• [BioC] LoadLibrary failures when loading RMySQL and xps packages   Marie Chehani Alles
• [BioC] Understanding limma, fdr and topTable   Naomi Altman
• [BioC] Understanding limma, fdr and topTable   Naomi Altman
• [BioC] Understanding limma, fdr and topTable   Naomi Altman
• [BioC] Raw, summarized intensity data from CEL files   Naomi Altman
• [BioC] confusion about nomenclature of illumina annotation packages   Lynn Amon
• [BioC] problem with read.table   Lynn Amon
• [BioC] confusion about nomenclature of illumina annotationpackages   Lynn Amon
• [BioC] illumina annotation packages vs. bgx manifests   Lynn Amon
• [BioC] illumina annotation packages vs. bgx manifests   Lynn Amon
• [BioC] Can't access biomaRt with mysql   Simon Anders
• [BioC] nested design with random factor and limma???   Bettina Kulle Andreassen
• [BioC] Two Color Array Expression   Antosh, Michael
• [BioC] Source code comments / read_abatch   Arkady
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Arkady
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Arkady
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Arkady
• [BioC] Error in RCurl and GEOquery installation   Elin Axelsson
• [BioC] regular expression for targets   Carlos J. Gil Bellosta
• [BioC] Pd info package affy 10K array   Henrik Bengtsson
• [BioC] Error in normalize.quantiles.robust   Henrik Bengtsson
• [BioC] Affxparser: how to create CEL-file from AffyBatch   Henrik Bengtsson
• [BioC] aroma.affymetrix and affy - different results   Henrik Bengtsson
• [BioC] inquiry for CDF file   Henrik Bengtsson
• [BioC] aroma.light advice sought   Henrik Bengtsson
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   Henrik Bengtsson
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   Henrik Bengtsson
• [BioC] ReadAffy crashes on mac   Henrik Bengtsson
• [BioC] ReadAffy crashes on mac   Henrik Bengtsson
• [BioC] Maximum number of CEL files for ReadAffy() in Affy package.   Henrik Bengtsson
• [BioC] limmaGUI: target file and spot file   Jamila Bernardi
• [BioC] LD plots   Boks, M.P.M.
• [BioC] Error in normalize.quantiles.robust   Ben Bolstad
• [BioC] ReadAffy crashes on mac   Ben Bolstad
• [BioC] rma for tiling arrays (oligo package)   Ben Bolstad
• [BioC] preprocessing for tiling arrays (preprocessCore package)   Ben Bolstad
• [BioC] Maximum number of CEL files for ReadAffy() in Affy package.   Ben Bolstad
• [BioC] Source code comments / read_abatch   Ben Bolstad
• [BioC] How to adjust the Heatmap.2 color key   Martin Bonke
• [BioC] How to adjust the Heatmap.2 color key   Martin Bonke
• [BioC] minor fitPLM bug in get.psi.code   Paul Boutros
• [BioC] LIMMA - fold change direction?   Glyn Bradley
• [BioC] how to test for genes of interest?   Glyn Bradley
• [BioC] how to test for genes of interest?   Glyn Bradley
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Siobhan A. Braybrook
• [BioC] Small RNAs database   Daniel Brewer
• [BioC] dev2bitmap error, 'gs' cannot be found   Boel Brynedal
• [BioC] Comparison of diff. t-statistics, Limma and rowttests   Boel Brynedal
• [BioC] Link to picture: Comparison of diff. t-statistics, Limma and rowttests   Boel Brynedal
• [BioC] Link to picture: Comparison of diff. t-statistics, Limma and rowttests   Boel Brynedal
• [BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2   Marc Carlson
• [BioC] ENSEMBL-centered annotations, how to?   Marc Carlson
• [BioC] Gene symbol converter/translator   Marc Carlson
• [BioC] Retrieving sequences from NCBI   Marc Carlson
• [BioC] Question about GOstatsHyperG   Marc Carlson
• [BioC] SQLForge and probes that map to multiple genes   Marc Carlson
• [BioC] error when using GOstats with AnnBuilder built package   Marc Carlson
• [BioC] SQLForge and probes that map to multiple genes   Marc Carlson
• [BioC] bovine Annotation package(s)   Marc Carlson
• [BioC] Gostats with Yeast annotation   Marc Carlson
• [BioC] Dmel. Gene Chip 2 tiling array CDF ; Drosophila melanogaster BDGP Release 5 annotation   Marc Carlson
• [BioC] rgug4130a   Marc Carlson
• [BioC] Bioconductor installation   Sean Cassidy
• [BioC] updateGraph & deprecated edgemode slot   Tony Chiang
• [BioC] EBImage library error   Tony Chiang
• [BioC] heatmap and cdfenv problems   Hui-Yi Chu
• [BioC] Understanding limma, fdr and topTable   Kevin R. Coombes
• [BioC] Agilent single color array   Mark Cowley
• [BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2   Mark Cowley
• [BioC] Blobs   Mark Cowley
• [BioC] Present/absent probes on miRNA arrays   Mark Cowley
• [BioC] Blobs   Mark Cowley
• [BioC] inquiry for CDF file   Mark Cowley
• [BioC] SQLForge and probes that map to multiple genes   Mark Cowley
• [BioC] SQLForge and probes that map to multiple genes   Mark Cowley
• [BioC] How to objectively evaluate chip quality?   Mark Cowley
• [BioC] Experimental Design, Model Matrix and Contrasts   Mark Cowley
• [BioC] limmaGUI: target file and spot file   Mark Cowley
• [BioC] Filtering probes without annotation prior to statistical test   Mark Cowley
• [BioC] Maximum number of CEL files for ReadAffy() in Affy package.   Hailong Cui
• [BioC] Adding a text label to the classvec colour bar in heatplot   Aedin Culhane
• [BioC] SFI Stokes Lecturer in computational biology (Ireland)   Aedin Culhane
• [BioC] inquiry for CDF file   Manhong Dai
• [BioC] Bioconductor Digest, Vol 65, Issue 23   Dai, Manhong
• [BioC] error using lumiR * correction   Kristen Dang
• [BioC] error using lumiR   Kristen K Dang
• [BioC] weighting chips   Sean Davis
• [BioC] gains and losses via mode shifting   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Sean Davis
• [BioC] Retrieving sequences from NCBI   Sean Davis
• [BioC] GEOquery error importing GEO data with 'null' values   Sean Davis
• [BioC] Question about GOstatsHyperG   Sean Davis
• [BioC] How to map a Sentrix BeadChip ID to BioC annotation package?   Sean Davis
• [BioC] problem with GEOquery   Sean Davis
• [BioC] Small RNAs database   Sean Davis
• [BioC] genefiltering before or after the normalization?   Sean Davis
• [BioC] Retrieving sequences from NCBI   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] genefiltering before or after the normalization?   Sean Davis
• [BioC] SQLForge and probes that map to multiple genes   Sean Davis
• [BioC] SQLForge and probes that map to multiple genes   Sean Davis
• [BioC] how to match tables   Sean Davis
• [BioC] Dealing with multiple probes per gene and multiple locations per probe.   Sean Davis
• [BioC] SQLForge and probes that map to multiple genes   Sean Davis
• [BioC] How to objectively evaluate chip quality?   Sean Davis
• [BioC] Memory problems analyzing 16 chips using arrayQualityMetrics package   Sean Davis
• [BioC] bovine Annotation package(s)   Sean Davis
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Sean Davis
• [BioC] problem with GDS2eSet   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] Question about Affymetrix High-density SNP arrays   Sean Davis
• [BioC] Howto Get GO/Gene-names of GEO-Soft Probe-names   Sean Davis
• [BioC] ArrayQuality package bug in agQuality function - marray package   Marcus Davy
• [BioC] limma: cannot repoduce older analysis   Marcus Davy
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   De Bondt, An-7114 [PRDBE]
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   De Bondt, An-7114 [PRDBE]
• [BioC] RSQLite error when using AnnotationDbi/SQLForge   Diego Diez
• [BioC] GEOquery error importing GEO data with 'null' values   Dreyfuss, Jonathan
• [BioC] Siggenes/SAM vs Excel   Jenny Drnevich
• [BioC] How to carry out time series analysis in Bioconductor   Jenny Drnevich
• [BioC] Understanding limma, fdr and topTable   Jenny Drnevich
• [BioC] How to adjust the Heatmap.2 color key   Jenny Drnevich
• [BioC] How to adjust the Heatmap.2 color key   Jenny Drnevich
• [BioC] regular expression for targets   Jenny Drnevich
• [BioC] genefiltering before or after the normalization?   Jenny Drnevich
• [BioC] LIMMA - fold change direction?   Jenny Drnevich
• [BioC] LIMMA: Duplicate spots   Jenny Drnevich
• [BioC] how to test for genes of interest?   Jenny Drnevich
• [BioC] how to test for genes of interest?   Jenny Drnevich
• [BioC] illumina annotation packages vs. bgx manifests   Pan Du
• [BioC] lumi question (About BeadStudio output columns)   Pan Du
• [BioC] lumi question (About BeadStudio output columns)   Pan Du
• [BioC] Present/absent probes on miRNA arrays   Heidi Dvinge
• [BioC] Missing summary in HTML reports   Heidi Dvinge
• [BioC] ENTREZ identifiers for PGSEA   Dykema, Karl
• [BioC] Siggenes/SAM Error   D F
• [BioC] Loading more than 16 annotation packages fails   Seth Falcon
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Christian Feller
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Christian Feller
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Christian Feller
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Christian Feller
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Christian Feller
• [BioC] Error in RCurl and GEOquery installation   Arnar Flatberg
• [BioC] Moe430A and Moe430B join   Matyas Flemr
• [BioC] LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)   Richard Friedman
• [BioC] Has GCRMA version 2.12 been benchmarked   Richard Friedman
• [BioC] weighting chips   DAVID ARTETA GARCIA
• [BioC] Error in normalize.quantiles.robust   DAVID ARTETA GARCIA
• [BioC] How to create an exprsSet from dataframe or matrix   DAVID ARTETA GARCIA
• [BioC] Error in normalize.quantiles.robust   DAVID ARTETA GARCIA
• [BioC] Error in normalize.quantiles.robust   DAVID ARTETA GARCIA
• [BioC] SOLVED Error in normalize.quantiles.robust   DAVID ARTETA GARCIA
• [BioC] vsn + backgroundSubtract   DAVID ARTETA GARCIA
• [BioC] vsn + backgroundSubtract   DAVID ARTETA GARCIA
• [BioC] regular expression for targets   DAVID ARTETA GARCIA
• [BioC] aroma.light advice sought   Iain Gallagher
• [BioC] P-values for tissue specific genes   Pascal Gellert
• [BioC] P-values for tissue specific genes   Pascal Gellert
• [BioC] P-values for tissue specific genes   Pascal Gellert
• [BioC] kOverA(k, A=100, na.rm=TRUE)   Robert Gentleman
• [BioC] cant install Rgraphviz   Robert Gentleman
• [BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2   Robert Gentleman
• [BioC] Rgraphviz on CRAN ??   Robert Gentleman
• [BioC] help with internet connection   Robert Gentleman
• [BioC] Small RNAs database   Robert Gentleman
• [BioC] problem with read.table   Robert Gentleman
• [BioC] Gostats with Yeast annotation   Robert Gentleman
• [BioC] ENTREZ identifiers for PGSEA   Sebastien Gerega
• [BioC] Adding a text label to the classvec colour bar in heatplot   Thomas Girke
• [BioC] molecular viz tools (eg, PyMol) and R?   Thomas Girke
• [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0   Ulrike Goebel
• [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0   Ulrike Goebel
• [BioC] limma background correction   Ulrike Goebel
• [BioC] help for pathways   Alberto Goldoni
• [BioC] LIMMA - problem with block analysis   Milena Gongora
• [BioC] Hopach and R-internal Heat-Mapping   Johannes Graumann
• [BioC] Problems installing bioconductor on ubuntu   Rebecca Griffiths
• [BioC] Gostats with Yeast annotation   Alex Gutteridge
• [BioC] Gostats with Yeast annotation   Alex Gutteridge
• [BioC] row maximum   Dr Balazs Gyorffy
• [BioC] how to match tables   Dr Balazs Gyorffy
• [BioC] bovine Annotation package(s)   Nathan S. Haigh
• [BioC] Siggenes/SAM vs Excel   Thomas Hampton
• [BioC] Affymetrix probeset ids to gene symbols   Thomas Hampton
• [BioC] Siggenes/SAM vs Excel   Thomas Hampton
• [BioC] X:Map and 1.0 ST Gene Arrays, Introns   Thomas Hampton
• [BioC] Agilent single color array   Kasper Daniel Hansen
• [BioC] Bioconductor installation   Kasper Daniel Hansen
• [BioC] vsn + backgroundSubtract   Kasper Daniel Hansen
• [BioC] Rgraphviz on CRAN ??   Kasper Daniel Hansen
• [BioC] Blobs   Kasper Daniel Hansen
• [BioC] P-values for tissue specific genes   Kasper Daniel Hansen
• [BioC] Affy array layout   Kasper Daniel Hansen
• [BioC] problem with read.table   Kasper Daniel Hansen
• [BioC] Adding a text label to the classvec colour bar in heatplot   Kasper Daniel Hansen
• [BioC] Error in slot assignment (Golub_Train exercise)   Tadayoshi Hari
• [BioC] Creating an expression set   Nathan Harmston
• [BioC] Dealing with multiple probes per gene and multiple locations per probe.   Nathan Harmston
• [BioC] HOPACH clustering of genes   Nathan Harmston
• [BioC] smlSet and snpMatrix / copy number analysis   Nathan Harmston
• [BioC] (no subject)   Jean Hausser
• [BioC] gcRMA on a GeneFeatureSet from Affy MoGene 1.0 ST v1?   Jean Hausser
• [BioC] Warnings after makePDpackage   Ann Hess
• [BioC] rma for tiling arrays (oligo package)   Ann Hess
• [BioC] preprocessing for tiling arrays (preprocessCore package)   Ann Hess
• [BioC] Affxparser: how to create CEL-file from AffyBatch   Hooiveld, Guido
• [BioC] ENSEMBL-centered annotations, how to?   Hooiveld, Guido
• [BioC] LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)   Hooiveld, Guido
• [BioC] Rgraphviz on CRAN ??   Kurt Hornik
• [BioC] Rgraphviz on CRAN ??   Kurt Hornik
• [BioC] vsn + backgroundSubtract   Wolfgang Huber
• [BioC] Hopach and R-internal Heat-Mapping   Wolfgang Huber
• [BioC] Problems installing bioconductor on ubuntu   Wolfgang Huber
• [BioC] genefiltering before or after the normalization?   Wolfgang Huber
• [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip   Wolfgang Huber
• [BioC] Differences in readExpressionSet between R2.7.1 and R2.5.1 version   Wolfgang Huber
• [BioC] how to match tables   Wolfgang Huber
• [BioC] limma: cannot repoduce older analysis   Wolfgang Huber
• [BioC] how to test for genes of interest?   Wolfgang Huber
• [BioC] Comparison of diff. t-statistics, Limma and rowttests   Wolfgang Huber
• [BioC] Link to picture: Comparison of diff. t-statistics, Limma and rowttests   Wolfgang Huber
• [BioC] Filtering probes without annotation prior to statistical test   Seungwoo Hwang
• [BioC] Raw, summarized intensity data from CEL files   Niels Høgslund
• [BioC] Rgraphviz on CRAN ??   Søren Højsgaard
• [BioC] Rgraphviz on CRAN ??   Søren Højsgaard
• [BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)   Paolo Innocenti
• [BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)   Paolo Innocenti
• [BioC] help for pathways   Saurin D. Jani
• [BioC] Converting to official gene symbols   Tu Kang
• [BioC] ?function to find minimum p value in matrix of probesets with duplicate gene ids   Mark Kimpel
• [BioC] affymetrix rat gene ST 1.0 cdf   Mark Kimpel
• [BioC] GSEA packages that depend on GSEABase?   Mark Kimpel
• [BioC] How to adjust the Heatmap.2 color key   Matthias Kohl
• [BioC] How to map a Sentrix BeadChip ID to BioC annotation package?   Christian Kohler
• [BioC] confusion about nomenclature of illumina annotation packages   Christian Kohler
• [BioC] illumina annotation packages vs. bgx manifests   Michal Kolář
• [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?   Chanchal Kumar
• [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?   Chanchal Kumar
• [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?   Chanchal Kumar
• [BioC] Categories microarray data in functional profiles   Marcelo Laia
• [BioC] Drosophila tiling array background correction   Benjamin Lansdell
• [BioC] Problem with makePDpackage in makePlatformDesign and getCdfInfo in affy   Benjamin Lansdell
• [BioC] Drosophila tiling array background correction   Benjamin Lansdell
• [BioC] Converting to official gene symbols   Charity Law
• [BioC] inquiry for CDF file   Lee, Hyeong-min
• [BioC] How to set "Pearson correlation " as similarity measure in qtclust() for doing QT cluster   Guiyuan Lei
• [BioC] How to set "Pearson correlation " as similarity measure in qtclust() for doing QT cluster   Guiyuan Lei
• [BioC] Question about "structure_exon_chrom_end" attributes in biomaRt   LiGang
• [BioC] how to get oligoSnpSet object?   Yupu Liang
• [BioC] Blobs   Steve Lianoglou
• [BioC] Problems installing bioconductor on ubuntu   Steve Lianoglou
• [BioC] Problems installing bioconductor on ubuntu   Steve Lianoglou
• [BioC] Small RNAs database   Steve Lianoglou
• [BioC] row maximum   Steve Lianoglou
• [BioC] Blobs   Steve Lianoglou
• [BioC] How to objectively evaluate chip quality?   Steve Lianoglou
• [BioC] Drosophila tiling array background correction   Steve Lianoglou
• [BioC] rma for tiling arrays (oligo package)   Steve Lianoglou
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Steve Lianoglou
• [BioC] Dmel. Gene Chip 2 tiling array CDF ; Drosophila melanogaster BDGP Release 5 annotation   Steve Lianoglou
• [BioC] gene expression using biopsies/mixtures of cell lines   Johan Lindberg
• [BioC] error when using GOstats with AnnBuilder built package   Johan Lindberg
• [BioC] discrepancy between limma and samr due to difference in fdr adjustment?   Johan Lindberg
• [BioC] discrepancy between limma and samr due to difference in fdr adjustment?   Johan Lindberg
• [BioC] discrepancy between limma and samr due to difference in fdr adjustment?   Johan Lindberg
• [BioC] Can limma be used to the matched data?   Chunyan Liu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] subset in XPS   Zhibin Lu
• [BioC] SPECIAL 20% OFF DISCOUNT ON A NEW BOOK FROM CRC PRESS   Senthil Kumar M
• [BioC] Understanding limma, fdr and topTable   James MacDonald
• [BioC] Understanding limma, fdr and topTable   James MacDonald
• [BioC] Understanding limma, fdr and topTable   James MacDonald
• [BioC] Affymetrix probeset ids to gene symbols   James MacDonald
• [BioC] ENTREZ identifiers for PGSEA   James MacDonald
• [BioC] Converting to official gene symbols   James MacDonald
• [BioC] Warnings after makePDpackage   James MacDonald
• [BioC] Source code comments / read_abatch   James MacDonald
• [BioC] Using ReadAffy with custom CDFs on tiling array data   James MacDonald
• [BioC] Maximum number of CEL files for ReadAffy() in Affy package.   James MacDonald
• [BioC] Error in normalize.quantiles.robust   James W. MacDonald
• [BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2   James W. MacDonald
• [BioC] Error in normalize.quantiles.robust   James W. MacDonald
• [BioC] Affxparser: how to create CEL-file from AffyBatch   James W. MacDonald
• [BioC] marray and limma error with lmFit-reg   James W. MacDonald
• [BioC] inquiry for CDF file   James W. MacDonald
• [BioC] Raw, summarized intensity data from CEL files   James W. MacDonald
• [BioC] Glycov3hscdf package   James W. MacDonald
• [BioC] rma for tiling arrays (oligo package)   James W. MacDonald
• [BioC] rma for tiling arrays (oligo package)   James W. MacDonald
• [BioC] Source code comments / read_abatch   James W. MacDonald
• [BioC] Using ReadAffy with custom CDFs on tiling array data   James W. MacDonald
• [BioC] Rat Gene 1.0 ST CDF files   James W. MacDonald
• [BioC] ?function to find minimum p value in matrix of probesets with duplicate gene ids   James W. MacDonald
• [BioC] affymetrix rat gene ST 1.0 cdf   James W. MacDonald
• [BioC] P-values for tissue specific genes   Sean MacEachern
• [BioC] Offre speciale   VoilesNews Magazine
• [BioC] Fwd: MySQL performance tuning   Pete Marchetto
• [BioC] Fwd: MySQL performance tuning   Pete Marchetto
• [BioC] Retrieving sequences from NCBI   J. Miguel Marin
• [BioC] LIMMA: Duplicate spots   Cecilia McGregor
• [BioC] Adding a text label to the classvec colour bar in heatplot   Mikhail, Amy
• [BioC] Adding a text label to the classvec colour bar in heatplot   Mikhail, Amy
• [BioC] Adding a text label to the classvec colour bar in heatplot   Mikhail, Amy
• [BioC] useMart alterations   Amanda Miotto
• [BioC] getBM local   Amanda Miotto
• [BioC] Error in RCurl and GEOquery installation   Momin, Amin A
• [BioC] Error in RCurl and GEOquery installation   Momin, Amin A
• [BioC] Cannot load preprocessCore.so   Martin Morgan
• [BioC] Error in normalize.quantiles.robust   Martin Morgan
• [BioC] An Sweave question   Martin Morgan
• [BioC] LoadLibrary failures when loading RMySQL and xps packages   Martin Morgan
• [BioC] Creating an expression set   Martin Morgan
• [BioC] biomaRt installation: unable to download XML library   Martin Morgan
• [BioC] Visualization of multiple alignments in bioconductor   Martin Morgan
• [BioC] species in MsigDB of GSEA   Martin Morgan
• [BioC] species in MsigDB of GSEA   Martin Morgan
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   Martin Morgan
• [BioC] Vignette for ShortRead   Martin Morgan
• [BioC] problem with read.table   Martin Morgan
• [BioC] problem with read.table   Martin Morgan
• [BioC] EBImage install: wsObjects() problem   Martin Morgan
• [BioC] P-values for tissue specific genes   Jose M Muino
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Naira Naouar
• [BioC] Using ReadAffy with custom CDFs on tiling array data   Naira Naouar
• [BioC] Avis de tempete sur les prix !   Voiles News
• [BioC] Deuxième vague de soldes !!!   Voiles News
• [BioC] Following meta-analysis, how to address type 2 error?   Ochsner, Scott A
• [BioC] gains and losses via mode shifting   Benjamin Otto
• [BioC] gains and losses via mode shifting   Benjamin Otto
• [BioC] gains and losses via mode shifting   Benjamin Otto
• [BioC] How to adjust the Heatmap.2 color key   Benjamin Otto
• [BioC] How to adjust the Heatmap.2 color key   Benjamin Otto
• [BioC] How to adjust the Heatmap.2 color key   Benjamin Otto
• [BioC] LIMMA: Duplicate spots   Philipp Pagel
• [BioC] limma: cannot repoduce older analysis   Philipp Pagel
• [BioC] limma: cannot repoduce older analysis   Philipp Pagel
• [BioC] problem with read.table   Herve Pages
• [BioC] LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)   Richard Pearson
• [BioC] Can't access biomaRt with mysql   Richard Pearson
• [BioC] vennDiagram in Limma   Francois Pepin
• [BioC] vennDiagram in Limma   James Perkins
• [BioC] DAnTE: Statistical Tool using R and R(D)COM   Ashoka Polpitiya
• [BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2   Christoph Preuss
• [BioC] hcluster crashes R environment   Henrique Proença
• [BioC] hcluster crashes R environment   Henrique Proença
• [BioC] snapCGH package - processCGH   Henrique Proença
• [BioC] limma background correction   Henrique Proença
• [BioC] limma background correction   Henrique Proença
• [BioC] REPRESENTATIVES NEEDED @ STEELBEL.BE   R.HIMPE
• [BioC] exonmap error & questions (Affy mouse exon arrays)   Wolfgang Raffelsberger
• [BioC] RSQLite error when using AnnotationDbi/SQLForge   Tim Rayner
• [BioC] RSQLite error when using AnnotationDbi/SQLForge   Tim Rayner
• [BioC] Surrogate variable analysis (SVA) with Limma   Augusto Rendon
• [BioC] Understanding limma, fdr and topTable   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] Understanding limma, fdr and topTable   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] siggenes and permutations   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] RMySQL   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] bovine Annotation package(s)   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] bovine Annotation package(s)   Louisa A Rispoli/AS/EXP/UTIA
• [BioC] beadarray - can't load data   Matt Ritchie
• [BioC] kOverA(k, A=100, na.rm=TRUE)   Roberts, Raymond
• [BioC] the function subset inside a function   Mark Robinson
• [BioC] aroma.affymetrix and affy - different results   Mark Robinson
• [BioC] biomaRt column order   Mark Robinson
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   Mark Robinson
• [BioC] useMart alterations   Mark Robinson
• [BioC] getBM local   Mark Robinson
• [BioC] Cannot load preprocessCore.so   Peter Robinson
• [BioC] Cannot load preprocessCore.so   Peter Robinson
• [BioC] Affymetrix probeset ids to gene symbols   Peter Robinson
• [BioC] Understanding limma, fdr and topTable   Robson, Samuel
• [BioC] plot overlay   David Ruau
• [BioC] plot overlay   David Ruau
• [BioC] simpleaffy pairwise.comparison problem   David Ruau
• [BioC] gains and losses via mode shifting   Oscar Rueda
• [BioC] gains and losses via mode shifting   Oscar Rueda
• [BioC] gains and losses via mode shifting   Oscar Rueda
• [BioC] gains and losses via mode shifting   Oscar Rueda
• [BioC] gains and losses via mode shifting   Oscar Rueda
• [BioC] gains and losses via mode shifting   Rueda.Oscar_Manuel
• [BioC] GEOquery   Harpreet Saini
• [BioC] Problems installing bioconductor on ubuntu   Bio Sam
• [BioC] cellHTS2 writeReport error   Becky Saunders
• [BioC] cellHTS2 writeReport error   Becky Saunders
• [BioC] the function subset inside a function   Lana Schaffer
• [BioC] the function subset inside a function   Lana Schaffer
• [BioC] combining samples before normalization   Lana Schaffer
• [BioC] aroma.affymetrix and affy - different results   Markus Schmidberger
• [BioC] Maximum number of CEL files for ReadAffy() in Affy package.   Markus Schmidberger
• [BioC] Visualization of multiple alignments in bioconductor   Schraga Schwartz
• [BioC] Siggenes/SAM Error   Holger Schwender
• [BioC] Siggenes/SAM vs Excel   Holger Schwender
• [BioC] Siggenes/SAM vs Excel   Holger Schwender
• [BioC] updateGraph & deprecated edgemode slot   Paul Shannon
• [BioC] molecular viz tools (eg, PyMol) and R?   Paul Shannon
• [BioC] HOPACH clustering of genes   Shannon, William
• [BioC] a customized GO term   Weiwei Shi
• [BioC] rgug4130a   Weiwei Shi
• [BioC] EBImage install: wsObjects() problem   Oleg Sklyar
• [BioC] limma background correction   Gordon K Smyth
• [BioC] nested design with random factor and limma???   Gordon K Smyth
• [BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)   Gordon K Smyth
• [BioC] how to test for genes of interest?   Gordon K Smyth
• [BioC] model.matrix()   Gordon K Smyth
• [BioC] Affymetrix probeset ids to gene symbols   Maria Stalteri
• [BioC] cant install Rgraphviz   Anders Stegmann
• [BioC] cant install Rgraphviz   Anders Stegmann
• [BioC] Drosophila tiling array background correction   Tobias Straub
• [BioC] Blobs   Yogi Sundaravadanam
• [BioC] Loading more than 16 annotation packages fails   Tarca, Adi
• [BioC] arrayQualityMetrics   Steve Taylor
• [BioC] SPECIAL 20% OFF DISCOUNT ON A NEW BOOK FROM CRC PRESS   Thomas, Judy
• [BioC] SPECIAL 20% OFF DISCOUNT ON A NEW BOOK FROM CRC PRESS   Thomas, Judy
• [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0   Joern Toedling
• [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0   Joern Toedling
• [BioC] regular expression for targets   Joern Toedling
• [BioC] Question about 'annFUN.db' in topGO ....   Joern Toedling
• [BioC] Gostats with Yeast annotation   Joern Toedling
• [BioC] Number or probes per target. Nimblegen arrays.   Joern Toedling
• [BioC] Error in slot assignment (Golub_Train exercise)   Joern Toedling
• [BioC] Job Opportunity at CBMI, Harvard Medical School   Tonellato, Peter
• [BioC] Gene symbol converter/translator   Anh Tran
• [BioC] Gene symbol converter/translator   Anh Tran
• [BioC] Nuse Axis   Paparountas Triantafyllos
• [BioC] Affymetrix probeset ids to gene symbols   Kurt Vanhoutte
• [BioC] high FDR_gene filter   Abhilash Venu
• [BioC] genefiltering before or after the normalization?   Abhilash Venu
• [BioC] genefiltering before or after the normalization?   Abhilash Venu
• [BioC] genefiltering before or after the normalization?   Abhilash Venu
• [BioC] genefiltering before or after the normalization?   Abhilash Venu
• [BioC] genefiltering before or after the normalization?   Abhilash Venu
• [BioC] Converting to official gene symbols   Gundala Viswanath
• [BioC] Howto Get GO/Gene-names of GEO-Soft Probe-names   Gundala Viswanath
• [BioC] ReadAffy crashes on mac   Luo Weijun
• [BioC] ReadAffy crashes on mac   Luo Weijun
• [BioC] ReadAffy crashes on mac   Luo Weijun
• [BioC] Two class paired analysis using siggenes   Mary Winn
• [BioC] species in MsigDB of GSEA   Di Wu
• [BioC] species in MsigDB of GSEA   Di Wu
• [BioC] LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)   Zhijin Wu
• [BioC] problem with GDS2eSet   Youngik Yang
• [BioC] 454 data normalization   Ziping Zhang
• [BioC] model.matrix()   Yisong Zhen
• [BioC] lumi question (About BeadStudio output columns)   Alison Ziesel
• [BioC] LIMMA Question: for lmFit   Yi Zou
• [BioC] How to create an exprsSet from dataframe or matrix   olszewski at atlas-biolabs.de
• [BioC] plot overlay   olszewski at atlas-biolabs.de
• [BioC] arrayQualityMetrics   audrey
• [BioC] Missing summary in HTML reports   simona dalle carbonare
• [BioC] Memory problems analyzing 16 chips using arrayQualityMetrics package   simona dalle carbonare
• [BioC] How to objectively evaluate chip quality?   simona dalle carbonare
• [BioC] Missing summary in HTML reports   simona dalle carbonare
• [BioC] An Sweave question   Nathan.Watson-Haigh at csiro.au
• [BioC] affyQCReport and +ve/-ve border elements   Nathan.Watson-Haigh at csiro.au
• [BioC] annotationTools incorrect use of ortholog   Nathan.Watson-Haigh at csiro.au
• [BioC] How to objectively evaluate chip quality?   Nathan.Watson-Haigh at csiro.au
• [BioC] bovine Annotation package(s)   Nathan.Watson-Haigh at csiro.au
• [BioC] Experimental Design, Model Matrix and Contrasts   Nathan.Watson-Haigh at csiro.au
• [BioC] Affy array layout   Nathan.Watson-Haigh at csiro.au
• [BioC] How to objectively evaluate chip quality?   Nathan.Watson-Haigh at csiro.au
• [BioC] Experimental Design, Model Matrix and Contrasts   Nathan.Watson-Haigh at csiro.au
• [BioC] Error in RCurl and GEOquery installation   Nathan.Watson-Haigh at csiro.au
• [BioC] subset in XPS   cstrato
• [BioC] subset in XPS   cstrato
• [BioC] LoadLibrary failures when loading RMySQL and xps packages   cstrato
• [BioC] subset in XPS   cstrato
• [BioC] subset in XPS   cstrato
• [BioC] subset in XPS   cstrato
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   cstrato
• [BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix   cstrato
• [BioC] affymetrix rat gene ST 1.0 cdf   cstrato
• [BioC] EBImage install: wsObjects() problem   colin davenport
• [BioC] Missing summary in HTML reports   audrey at ebi.ac.uk
• [BioC] arrayQualityMetrics   audrey at ebi.ac.uk
• [BioC] LIMMA - fold change direction?   J.delasHeras at ed.ac.uk
• [BioC] Number or probes per target. Nimblegen arrays.   J.delasHeras at ed.ac.uk
• [BioC] limmaGUI: target file and spot file   J.delasHeras at ed.ac.uk
• [BioC] St. Jude's Ross Et al. (2003) dataset in ExpressionSet form?   aoron at fhcrc.org
• [BioC] Dmel. Gene Chip 2 tiling array CDF ; Drosophila melanogaster BDGP Release 5 annotation   mythilyg ganapathi
• [BioC] Subtracting batch effect with Limma   pchristoph at gmail.com
• [BioC] Understanding limma, fdr and topTable   aaron.j.mackey at gsk.com
• [BioC] Understanding limma, fdr and topTable   aaron.j.mackey at gsk.com
• [BioC] help with internet connection   joanne.m.cox at gsk.com
• [BioC] error asMatrixWeights in LimmaGUI   bzzandrew at interfree.it
• [BioC] Vignette for ShortRead   joseph
• [BioC] help in ScanArray Express   lau pel
• [BioC] Rat Gene 1.0 ST CDF files   cunye qiao
• [BioC] marray and limma error with lmFit-reg   sabitha ramanathan
• [BioC] cellHTS2 writeReport error   rclement
• [BioC] cellHTS2 writeReport error   rclement
• [BioC] limma contrasts   renns
• [BioC] limma contrasts   renns
• [BioC] aroma.affymetrix and affy - different results   schmidi
• [BioC] aroma.affymetrix and affy - different results   schmidi
• [BioC] read.maimages, file is not in Axon Text File (ATF) format   Deafening silence
• [BioC] read.maimages, file is not in Axon Text File (ATF) format   Deafening silence
• [BioC] Glycov3hscdf package   Harmeet singh
• [BioC] Question about GOstatsHyperG   ss
• [BioC] Question about GOstatsHyperG   ss
• [BioC] Question about GOstatsHyperG   ss
• [BioC] A question about criteria for calling gain and loss in aCGH data   ss
• [BioC] Question about Affymetrix High-density SNP arrays   ss
• [BioC] Fwd: biomaRt column order   steffen at stat.Berkeley.EDU
• [BioC] [ Re: Fwd: biomaRt column order]   steffen at stat.Berkeley.EDU
• [BioC] Fwd: biomaRt column order   steffen at stat.Berkeley.EDU
• [BioC] Help in BioMart   steffen at stat.Berkeley.EDU
• [BioC] getBM local   steffen at stat.Berkeley.EDU
• [BioC] How to create an exprsSet from dataframe or matrix   anna freni sterrantino
• [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?   anna freni sterrantino
• [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?   anna freni sterrantino
• [BioC] beadarray - can't load data   Zoe.VanHavre at student.griffith.edu.au
• [BioC] biomaRt installation: unable to download XML library   raffaele.calogero at unito.it
• [BioC] problem with read.table   carol white
• [BioC] problem with read.table   carol white
• [BioC] R/S-Plus Fundamentals and Programming Techniques course in *** New YorkCity*** July 28-29 by XLSolutions Corp   sue at xlsolutions-corp.com
• [BioC] 2 Courses*** R/Splus Advanced Programming : August 14-15 in Seattle ! byXLSolutions Corp   sue at xlsolutions-corp.com
• [BioC] How to carry out time series analysis in Bioconductor   yemi yomi
• [BioC] EBImage library error   marco zucchelli
• [BioC] EBImage library error   marco zucchelli
• [BioC] Illumina HumanWG6 vs. HumanHT-12   Ingrid H. G. Østensen

Last message date: Thu Jul 31 22:47:27 CEST 2008
Archived on: Thu Jul 31 22:47:53 CEST 2008

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