May 2010 Archives by author

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Starting: Sat May 1 00:48:59 CEST 2010
Ending: Mon May 31 23:47:18 CEST 2010
Messages: 548

• [BioC] Validated miRNAs revisited   michael watson (IAH-C)
• [BioC] Validated miRNAs revisited   michael watson (IAH-C)
• [BioC] GEOquery: invalid class "ExpressionSet" object: featureNames differ between assayData and featureData   michael watson (IAH-C)
• [BioC] Human, Mouse and Rat homologs   michael watson (IAH-C)
• [BioC] Experimental design for RNA-Seq   michael watson (IAH-C)
• [BioC] Experimental design for RNA-Seq   michael watson (IAH-C)
• [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   michael watson (IAH-C)
• [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   michael watson (IAH-C)
• [BioC] Experimental design for RNA-Seq   michael watson (IAH-C)
• [BioC] function symbol not found (was Re: seqselect function in IRanges not working)   Patrick Aboyoun
• [BioC] function symbol not found (was Re: seqselect function in IRanges not working)   Patrick Aboyoun
• [BioC] IRanges bug? Running do.cal("c", list.of.IRanges.objects)   Patrick Aboyoun
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Patrick Aboyoun
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Patrick Aboyoun
• [BioC] Rgraphviz crashes Windows   Sancar Adali
• [BioC] Rgraphviz crashes Windows   Sancar Adali
• [BioC] [Rgraphviz] Xfig file export bug   Sancar Adali
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   Naomi Altman
• [BioC] Experimental design for RNA-Seq   Naomi Altman
• [BioC] GOstats - zebrafish   Neel Aluru
• [BioC] AgiMicroRna - FilterMicroRna and SignificantMicroRna function   Neel Aluru
• [BioC] question about qc function in SimpleAffy package with U95Av2 array   James Anderson
• [BioC] question about qc function in SimpleAffy package with U95Av2 array   James Anderson
• [BioC] Lumi mouse mapping   Antonina Mitrofanova, PhD
• [BioC] Design matrix for time course analysis with maSigPro   Matthias Boeck
• [BioC] Problems in MAplot for affybatch objects   Ben Bolstad
• [BioC] limma, duplicateCorrelation, dupfit$consensus = 1: concerning?   Karl Brand
• [BioC] limma, duplicateCorrelation, dupfit$consensus = 1: concerning?   Karl Brand
• [BioC] Affy exon array equivalents of QC packages (affyPLM, arrayQualityMetrics & affyQCReport)   Daniel Brewer
• [BioC] LIMMA: Suitable measure of error from result object. stdev.unscaled?   Daniel Brewer
• [BioC] problem in installing simpleaffy packeges   NUTAN CHAUHAN
• [BioC] Romer and symbols2indices query   Vincent Carey
• [BioC] annaffy-like HTML autput for org.Hs.eg.db and similar metadata packages   Vincent Carey
• [BioC] Lumi annotation mapping in lumiR: nuID error   Vincent Carey
• [BioC] Error when running script on latest BioC: "ExpressionSet" object: sampleNames differ between phenoData and protocolData   Vincent Carey
• [BioC] remapping the SNPs in the Affy6.0   Vincent Carey
• [BioC] remapping the SNPs in the Affy6.0   Vincent Carey
• [BioC] pint   Vincent Carey
• [BioC] Copy number variation   Vincent Carey
• [BioC] code improvements   Vincent Carey
• [BioC] edgeWeights of a distGraph object   Vincent Carey
• [BioC] code improvements   Vincent Carey
• [BioC] help with illumina microarray (DASL)   Vincent Carey
• [BioC] AnnotationDbi quesion please help   Vincent Carey
• [BioC] (no subject)   Vincent Carey
• [BioC] anybody parsing BioPAX 2?   Vincent Carey
• [BioC] Mapping NCBI accession numbers to GO terms   Vincent Carey
• [BioC] question about qc function in SimpleAffy package with U95Av2 array   Vincent Carey
• [BioC] How to show the definition of readFastq   Vincent Carey
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Vincent Carey
• [BioC] exon array Problem   Vincent Carey
• [BioC] finding and deleting repeated observations   Vincent Carey
• [BioC] mogene10stv1 annotation problem   Vincent Carey
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Marc Carlson
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Marc Carlson
• [BioC] Illumina annotation   Marc Carlson
• [BioC] Lumi annotation mapping in lumiR: nuID error   Marc Carlson
• [BioC] Query regarding for Entrez IDpackage   Marc Carlson
• [BioC] lumi annotation using nuID, missing gene symbols   Marc Carlson
• [BioC] GEO annotations   Marc Carlson
• [BioC] Query regarding entrez id   Marc Carlson
• [BioC] Query regarding entrez id   Marc Carlson
• [BioC] annotating reads acording with position on mapping   Marc Carlson
• [BioC] GOstats/Category hyperGTest gene universe problem   Marc Carlson
• [BioC] hugene10stprobeset   Marc Carlson
• [BioC] BioC 2.6 - changelog for individual packages?   Benilton Carvalho
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Benilton Carvalho
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Benilton Carvalho
• [BioC] Human Gene ST using oligo package   Benilton Carvalho
• [BioC] Human Gene ST using oligo package   Benilton Carvalho
• [BioC] Human Gene ST using oligo package   Benilton Carvalho
• [BioC] Human Gene ST using oligo package   Benilton Carvalho
• [BioC] pdInfoBuilder -- MOUSEDIVm520650   Benilton Carvalho
• [BioC] Question about beadarray package for mouse ref V2 illumina beadarray   Yiwen Chen
• [BioC] lumi annotation using nuID, missing gene symbols   John Coulthard
• [BioC] PR, topGene and 'gene.names should have the same length as the gene vector'   John Coulthard
• [BioC] mogene10stv1 annotation problem   Dave Crawford
• [BioC] mogene10stv1 annotation problem   Dave Crawford
• [BioC] Query regarding Clustering   Sean Davis
• [BioC] R: Validated miRNAs revisited   Sean Davis
• [BioC] Error using GEOquery package   Sean Davis
• [BioC] Bioconductor GEOquery package error   Sean Davis
• [BioC] Bioconductor GEOquery package error   Sean Davis
• [BioC] Help with the terminology   Sean Davis
• [BioC] Query regarding Bioconductor   Sean Davis
• [BioC] Obtaining Normalised Signal intensities   Sean Davis
• [BioC] Obtaining Normalised Signal intensities   Sean Davis
• [BioC] Query regarding entrez id   Sean Davis
• [BioC] GEO annotations   Sean Davis
• [BioC] GEO annotations   Sean Davis
• [BioC] GEO annotations   Sean Davis
• [BioC] Query regarding entrez id   Sean Davis
• [BioC] GDS normalization   Sean Davis
• [BioC] GEO annotations   Sean Davis
• [BioC] Query regarding entrez id   Sean Davis
• [BioC] reading a .psl file   Sean Davis
• [BioC] reading a .psl file   Sean Davis
• [BioC] help with affy annotation   Sean Davis
• [BioC] help with annaffy package   Sean Davis
• [BioC] R: Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   Sean Davis
• [BioC] R: R: Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   Sean Davis
• [BioC] Reg: GEO query using R package   Sean Davis
• [BioC] Query regarding Contrasts desigs   Sean Davis
• [BioC] Query regarding Contrasts desigs   Sean Davis
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Sean Davis
• [BioC] [Bioc-devel] Problem with merge   Sean Davis
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Sean Davis
• [BioC] kmeans clustering and gene names; was Re: Bioconductor Digest, Vol 87, Issue 10   Sean Davis
• [BioC] Error in lm.fit(design, t(M)) from GEO dataset   Sean Davis
• [BioC] GEOquery getGEO "error in scan"   Sean Davis
• [BioC] question about CDF file   Sean Davis
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   Sean Davis
• [BioC] after updating biomaRt cannot connect any more   Sean Davis
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   Sean Davis
• [BioC] status of the DAVIDQuery package   Day, Roger S
• [BioC] code improvements   Mike Dewar
• [BioC] code improvements   Mike Dewar
• [BioC] Applying classifiers derived from CMA   Mike Dewar
• [BioC] Copy number variation   Ramon Diaz-Uriarte
• [BioC] Error using getMeans function in Ringo/Starr   Noah Dowell
• [BioC] Error using getMeans function in Ringo/Starr   Noah Dowell
• [BioC] Error using getMeans function in Ringo/Starr   Noah Dowell
• [BioC] Reading .bpmap files for homemade tiling arrays   Noah Dowell
• [BioC] help with illumina microarray (DASL)   Pan Du
• [BioC] help with lumi   Pan Du
• [BioC] ShortRead information   Jennifer Dupiot
• [BioC] Human, Mouse and Rat homologs   Steffen Durinck
• [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   Steffen Durinck
• [BioC] HTqPCR (plotCtOverview) problem   Heidi Dvinge
• [BioC] htqPCR question   Heidi Dvinge
• [BioC] htqPCR question   Heidi Dvinge
• [BioC] HTqPCR (plotCtOverview) problem   Heidi Dvinge
• [BioC] Questions about using Limma   Heidi Dvinge
• [BioC] HTqPCR setCategories problem   Heidi Dvinge
• [BioC] HTqPCR setCategories problem   Heidi Dvinge
• [BioC] Follow-up -> ERROR: caught BioMart::Exception:   Heidi Dvinge
• [BioC] sir   Heidi Dvinge
• [BioC] Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   Heidi Dvinge
• [BioC] HTqPCR: weird error and wrong feature positions after limma.CtData   Heidi Dvinge
• [BioC] Reading in data with HTqPCR   Heidi Dvinge
• [BioC] Reading in data with HTqPCR   Heidi Dvinge
• [BioC] after updating biomaRt cannot connect any more   Heidi Dvinge
• [BioC] Reading in data with HTqPCR   Heidi Dvinge
• [BioC] Call for papers: BCBGC-10, USA, July 2010   John Edward
• [BioC] FW: SetMethod for Combine   Mercier Eloi
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer warning serious? and nrot=9999?   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Romer warning serious? and nrot=9999?   Loren Engrav
• [BioC] Romer and symbols2indices query   Loren Engrav
• [BioC] Limma: nested design: coefficient not estimable ?   F F
• [BioC] Limma: nested design: coefficient not estimable ?   F F
• [BioC] segfault with rmaMicroRna in AgiMicroRna package   Seth Falcon
• [BioC] pulling functional information for SNPs   Seth Falcon
• [BioC] org.Hs.eg.db   Seth Falcon
• [BioC] Reg: hopach clustering   Rohit Farmer
• [BioC] Lumi annotation mapping in lumiR: nuID error   Gilbert Feng
• [BioC] lumi annotation using nuID, missing gene symbols   Gilbert Feng
• [BioC] Lumi mouse mapping   Gilbert Feng
• [BioC] anybody parsing BioPAX 2?   Gilbert Feng
• [BioC] tool for drawing interaction network   Gilbert Feng
• [BioC] help with lumi   Gilbert Feng
• [BioC] annotating lumi   Gilbert Feng
• [BioC] Control based normalization   Chris Fenton
• [BioC] Plotting trees - hclust object vs dendrogram   Anthony Ferrari
• [BioC] tree manipulation   Anthony Ferrari
• [BioC] tree manipulation   Anthony Ferrari
• [BioC] Collaborators   Alexandru Floares
• [BioC] Sequence analysis techniques in Bioconductor   Javier Pérez Florido
• [BioC] Human Gene ST using oligo package   Javier Pérez Florido
• [BioC] Human Gene ST using oligo package   Javier Pérez Florido
• [BioC] htqPCR question   Andreia Fonseca
• [BioC] htqPCR question   Andreia Fonseca
• [BioC] annotating reads acording with position on mapping   Andreia Fonseca
• [BioC] HTqPCR: weird error and wrong feature positions after limma.CtData   Andreia Fonseca
• [BioC] HTqPCR: weird error and wrong feature positions after limma.CtData   Andreia Fonseca
• [BioC] pint   Raquel Mart’inez Garc’ia
• [BioC] pint   Raquel Mart’inez Garc’ia
• [BioC] pint   Raquel Mart’inez Garc’ia
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Laurent Gautier
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Laurent Gautier
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Laurent Gautier
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Laurent Gautier
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   Laurent Gautier
• [BioC] Error installing Rsamtools   Paul Geeleher
• [BioC] Error installing Rsamtools   Paul Geeleher
• [BioC] Alignment viewer?   Thomas Girke
• [BioC] tree manipulation   Thomas Girke
• [BioC] Aligned RNA-seq data to ranked list of genes   Thomas Girke
• [BioC] Starr - MAT normalization   Raphael Gottardo
• [BioC] FW: Mas5 works with mm set on NA?   Groot, Philip de
• [BioC] makeAttr() missing in KEGGgraph   Groot, Philip de
• [BioC] Lumi annotation mapping in lumiR: nuID error   Thomas Hampton
• [BioC] Rgraphviz crashes Windows   Kasper Daniel Hansen
• [BioC] Unique CDF File   Kasper Daniel Hansen
• [BioC] Saving/loading Genominator ExpData-class object   Kasper Daniel Hansen
• [BioC] Saving/loading Genominator ExpData-class object   Kasper Daniel Hansen
• [BioC] Genominator question   Kasper Daniel Hansen
• [BioC] Aligned RNA-seq data to ranked list of genes   Kasper Daniel Hansen
• [BioC] Non-specific filtering for HyperGeometric/GSEA test   Yuan Hao
• [BioC] Non-specific filtering for HyperGeometric/GSEA test   Yuan Hao
• [BioC] Experimental design for RNA-Seq   Jakob Hedegaard
• [BioC] microarray data without replication   Ina Hoeschele
• [BioC] Fwd: microarray data without replication   Ina Hoeschele
• [BioC] tool for drawing interaction network   Hooiveld, Guido
• [BioC] RGraphViz: length edges   Hooiveld, Guido
• [BioC] Unable to get the Platform Table using fData on eset object   Wolfgang Huber
• [BioC] Bioconductor Developer Meeting - Heidelberg 17./18. Nov 2010   Wolfgang Huber
• [BioC] tree manipulation   Wolfgang Huber
• [BioC] Non-specific filtering for HyperGeometric/GSEA test   Wolfgang Huber
• [BioC] ArrayExpress User Survey   Wolfgang Huber
• [BioC] Human, Mouse and Rat homologs   Wolfgang Huber
• [BioC] batch effect   Wolfgang Huber
• [BioC] Aligned RNA-seq data to ranked list of genes   Wolfgang Huber
• [BioC] What to do with this data? Question on deconfouding and GO analysis   Wolfgang Huber
• [BioC] Design matrix for time course analysis with maSigPro   Wolfgang Huber
• [BioC] Reg: hopach clustering   Wolfgang Huber
• [BioC] BioC 2.6 - changelog for individual packages?   Michael Imbeault
• [BioC] tool for drawing interaction network   Michael Imbeault
• [BioC] lattice and base-graphics using gridBase   Maarten van Iterson
• [BioC] lattice and base-graphics using gridBase   Maarten van Iterson
• [BioC] Mouse diversity array --building the required files for aroma.affymetrix UGP, UFL   Ivanek, Robert
• [BioC] pdInfoBuilder -- MOUSEDIVm520650   Ivanek, Robert
• [BioC] remapping the SNPs in the Affy6.0   Kay Jaja
• [BioC] Copy number variation   Kay Jaja
• [BioC] copy number variation   Kay Jaja
• [BioC] Agi4x44PreProcess Problem   Janszen, Derek B
• [BioC] [maSigPro] get.siggenes, PlotGroups - results   Maciej Jończyk
• [BioC] Illumina annotation   Katie
• [BioC] help with affy annotation   Katie
• [BioC] Two bioinformatics positions in Bordeaux, France   Audrey Kauffmann
• [BioC] finding and deleting repeated observations   Mervi Kinnunen
• [BioC] Starr - MAT normalization   Hans-Ulrich Klein
• [BioC] Error: invalid DB schema version (found 2.0, expected 2.1)   Christian Kohler
• [BioC] Error: invalid DB schema version (found 2.0, expected 2.1)   Christian Kohler
• [BioC] anybody parsing BioPAX 2?   Ossi Koivistoinen
• [BioC] code improvements   Kuhn, Alexandre (NIH/NIA/IRP) [V]
• [BioC] edgeWeights of a distGraph object   Burak Kutlu
• [BioC] graph/graphNEL: edge properties from edge name   Gustavo Lacerda
• [BioC] pint (& segmentation)   Leo Lahti
• [BioC] rtracklayer - getTable   Michael Lawrence
• [BioC] Alignment viewer?   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] loop over IRanges spaces   Michael Lawrence
• [BioC] rtracklayer GraphTrackLine   Michael Lawrence
• [BioC] Agilent arrays missing spots   Michael Lawrence
• [BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)   Michael Lawrence
• [BioC] anybody parsing BioPAX 2?   Michael Lawrence
• [BioC] tool for drawing interaction network   Michael Lawrence
• [BioC] RGraphViz: length edges   Michael Lawrence
• [BioC] Building AnnotationDbi Packages - Problems when using makeAnnDbPkg   Julian Lee
• [BioC] Help with the terminology   Steve Lianoglou
• [BioC] Manipulating large DNAStringSet(s)   Steve Lianoglou
• [BioC] Manipulating large DNAStringSet(s)   Steve Lianoglou
• [BioC] IRanges bug? Running do.cal("c", list.of.IRanges.objects)   Steve Lianoglou
• [BioC] IRanges bug? Running do.cal("c", list.of.IRanges.objects)   Steve Lianoglou
• [BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)   Steve Lianoglou
• [BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)   Steve Lianoglou
• [BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)   Steve Lianoglou
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Steve Lianoglou
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   Steve Lianoglou
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   Steve Lianoglou
• [BioC] Experimental design for RNA-Seq   Steve Lianoglou
• [BioC] Experimental design for RNA-Seq   Steve Lianoglou
• [BioC] Experimental design for RNA-Seq   Steve Lianoglou
• [BioC] org.Hs.eg.db   Uwe Ligges
• [BioC] org.Hs.eg.db   Uwe Ligges
• [BioC] org.Hs.eg.db   Uwe Ligges
• [BioC] Obtaining Normalised Signal intensities   Lloyd, Bryony
• [BioC] annaffy-like HTML autput for org.Hs.eg.db and similar metadata packages   Claudio Lottaz
• [BioC] database schemas   David Lyon
• [BioC] hugene10stprobeset   David Lyon
• [BioC] AnnotationDbi quesion please help   David Lyon
• [BioC] AnnotationDbi quesion please help   David Lyon
• [BioC] AnnotationDbi quesion please help   David Lyon
• [BioC] package ‘hugene11sttranscriptcluster.db’ is not available   David Lyon
• [BioC] package ‘hugene11sttranscriptcluster.db’ is not available   David Lyon
• [BioC] package ‘hugene11sttranscriptcluster.db’ is not available   David Lyon
• [BioC] Human, Mouse and Rat homologs   David Lyon
• [BioC] Human, Mouse and Rat homologs   David Lyon
• [BioC] Human, Mouse and Rat homologs   David Lyon
• [BioC] help: limma and changing gene results!   James MacDonald
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   James W. MacDonald
• [BioC] visualization of Loess smoothing curve   James W. MacDonald
• [BioC] R: visualization of Loess smoothing curve   James W. MacDonald
• [BioC] pulling functional information for SNPs   James W. MacDonald
• [BioC] pulling functional information for SNPs   James W. MacDonald
• [BioC] Questions about using Limma   James W. MacDonald
• [BioC] seqselect function in IRanges not working   James W. MacDonald
• [BioC] GOstats - zebrafish   James W. MacDonald
• [BioC] org.Hs.eg.db   James W. MacDonald
• [BioC] lattice and base-graphics using gridBase   James W. MacDonald
• [BioC] help: limma and changing gene results!   James W. MacDonald
• [BioC] code improvements   James W. MacDonald
• [BioC] AFFX probes as result of differential expression analysis   James W. MacDonald
• [BioC] Query ERROR: caught BioMart::Exception   James W. MacDonald
• [BioC] help with multtest and annaffy   James W. MacDonald
• [BioC] help: limma and changing gene results!   James W. MacDonald
• [BioC] Query regarding limma package   James W. MacDonald
• [BioC] Aligned RNA-seq data to ranked list of genes   James W. MacDonald
• [BioC] exon array Problem   James W. MacDonald
• [BioC] RMA without probe summarization   James W. MacDonald
• [BioC] pdInfoBuilder -- MOUSEDIVm520650   James W. MacDonald
• [BioC] Reading in data with HTqPCR   James W. MacDonald
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Lilyana Margaretha
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Lilyana Margaretha
• [BioC] help: limma and changing gene results!   Koen Marien
• [BioC] help: limma and changing gene results!   Koen Marien
• [BioC] help: limma and changing gene results!   Koen Marien
• [BioC] help: limma and changing gene results!   Koen Marien
• [BioC] seqselect function in IRanges not working   Fahim Md
• [BioC] function symbol not found (was Re: seqselect function in IRanges not working)   Fahim Md
• [BioC] reading a .psl file   Fahim Md
• [BioC] reading a .psl file   Fahim Md
• [BioC] visualization of Loess smoothing curve   Erika Melissari
• [BioC] I: visualization of Loess smoothing curve   Erika Melissari
• [BioC] (no subject)   Swapna Menon
• [BioC] Unique CDF File   Milner, Danny A.,Jr.,M.D.
• [BioC] Aligned RNA-seq data to ranked list of genes   L. Mohammadi
• [BioC] Aligned RNA-seq data to ranked list of genes   L. Mohammadi
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Saroj K Mohapatra
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Saroj K Mohapatra
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Saroj K Mohapatra
• [BioC] Romer and symbols2indices query   Martin Morgan
• [BioC] Error compiling affyio - undefined symbol: egzread   Martin Morgan
• [BioC] PR, topGene and 'gene.names should have the same length as the gene vector'   Martin Morgan
• [BioC] help with annaffy package   Martin Morgan
• [BioC] BioC 2010 Afternoon Practical Proposals   Martin Morgan
• [BioC] Help with PlateCore   Martin Morgan
• [BioC] package ‘hugene11sttranscriptcluster.db’ is not available   Martin Morgan
• [BioC] package ‘hugene11sttranscriptcluster.db’ is not available   Martin Morgan
• [BioC] Mapping NCBI accession numbers to GO terms   Martin Morgan
• [BioC] problem in installing simpleaffy packeges   Martin Morgan
• [BioC] How to show the definition of readFastq   Martin Morgan
• [BioC] FW: SetMethod for Combine   Martin Morgan
• [BioC] How to see XStringSet's definition?   Martin Morgan
• [BioC] How to show the definition of readFastq   Martin Morgan
• [BioC] Typo in ?FastqQuality help page?   Martin Morgan
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Martin Morgan
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Martin Morgan
• [BioC] REVISED BioC 2010 Scholarship Application due date   Martin Morgan
• [BioC] Problem with createAnnObjs.HUMANCHIP_DB   Martin Morgan
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Martin Morgan
• [BioC] makeAttr() missing in KEGGgraph   Martin Morgan
• [BioC] ShortRead information   Martin Morgan
• [BioC] Error installing Rsamtools   Martin Morgan
• [BioC] Error: invalid DB schema version (found 2.0, expected 2.1)   Martin Morgan
• [BioC] Error installing Rsamtools   Martin Morgan
• [BioC] HTqPCR (plotCtOverview) problem   Michael Muratet
• [BioC] HTqPCR setCategories problem   Michael Muratet
• [BioC] HTqPCR setCategories problem   Michael Muratet
• [BioC] HTqPCR setCategories problem   Michael Muratet
• [BioC] HTqPCR setCategories problem   Michael Muratet
• [BioC] Getting qPCRset with replicates   Michael Muratet
• [BioC] lattice and base-graphics using gridBase   Paul Murrell
• [BioC] limma 2x2 factorial contrast.matrix   Ben Nota
• [BioC] Rgraphviz crashes Windows   Hervé Pagès
• [BioC] Manipulating large DNAStringSet(s)   Hervé Pagès
• [BioC] Error in loading "IRanges" package (version 1.6.1)   Hervé Pagès
• [BioC] 11 more packages available on 64-bit Windows   Hervé Pagès
• [BioC] flowCore and curvHDR   Albert Park
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Richard Pearson
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Richard Pearson
• [BioC] Bioconductor Digest, Vol 87, Issue 10   Richard Pearson
• [BioC] Fwd: microarray data without replication   Richard Pearson
• [BioC] Agilent arrays missing spots   Francois Pepin
• [BioC] Reg: GEO query using R package   Ramani
• [BioC] draw more than one gate on a yxplot (flowViz)   Manuel Ramon
• [BioC] GOstats/Category hyperGTest gene universe problem   James F. Reid
• [BioC] GEOquery, GSE, and MAList   James F. Reid
• [BioC] Mapping NCBI accession numbers to GO terms   James F. Reid
• [BioC] Error in lm.fit(design, t(M)) from GEO dataset   James F. Reid
• [BioC] Romer and symbols2indices query   Matthew Ritchie
• [BioC] Help with plateCore   Sancho, Jose
• [BioC] Help with PlateCore   Sancho, Jose
• [BioC] Help with PlateCore   Sancho, Jose
• [BioC] Error compiling affyio - undefined symbol: egzread   Neil Saunders
• [BioC] Error compiling affyio - undefined symbol: egzread   Neil Saunders
• [BioC] Error compiling affyio - undefined symbol: egzread [SOLVED]   Neil Saunders
• [BioC] Error in lm.fit(design, t(M)) from GEO dataset   Jeremiah H. Savage
• [BioC] AFFX probes as result of differential expression analysis   Constanze Schmitt
• [BioC] anybody parsing BioPAX 2?   Paul Shannon
• [BioC] anybody parsing BioPAX 2?   Paul Shannon
• [BioC] Bioconductor GEOquery package error   Rahul Sharma
• [BioC] Error using GEOquery package   Rahul Sharma
• [BioC] help with SPIA package   Barbara Bo-Ju Shih
• [BioC] doubt about samr siggenes.table$genes.up   Leonardo K. Shikida
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Shuying
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Shuying
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Shuying
• [BioC] Reading .bpmap files for homemade tiling arrays   Larry Singh
• [BioC] Agi4x44PreProcess Problem   Smirnov, Ivan
• [BioC] Human Gene ST using oligo package   Mike Smith
• [BioC] Romer and symbols2indices query   Gordon K Smyth
• [BioC] Romer warning serious? and nrot=9999?   Gordon K Smyth
• [BioC] Romer and symbols2indices query   Gordon K Smyth
• [BioC] Romer and symbols2indices query   Gordon K Smyth
• [BioC] LIMMA: Suitable measure of error from result object. stdev.unscaled?   Gordon K Smyth
• [BioC] Using Limma for peptide array analysis - technical replicate issues and false positives   Gordon K Smyth
• [BioC] limma, duplicateCorrelation, dupfit$consensus = 1   Gordon K Smyth
• [BioC] Using Limma for peptide array analysis - technical replicate issues and false positives   Gordon K Smyth
• [BioC] Help with plateCore   Errol Strain
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] rtracklayer GraphTrackLine   Dario Strbenac
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Dario Strbenac
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Dario Strbenac
• [BioC] ChIPpeakAnno Critical Bug   Dario Strbenac
• [BioC] ChIPpeakAnno Critical Bug   Dario Strbenac
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Dario Strbenac
• [BioC] ChIPpeakAnno: New Features: distance calculation based on user selection of location of the peak and location of feature   Dario Strbenac
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Dario Strbenac
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Dario Strbenac
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Dario Strbenac
• [BioC] Error: formal argument "envir" matched by multiple actual arguments   Shuying Sun
• [BioC] Error when running script on latest BioC: "ExpressionSet" object: sampleNames differ between phenoData and protocolData   Dirk Swanevelder
• [BioC] limma help - choosing an approach   Tan, Yifang
• [BioC] LIMMA   Tan, Yifang
• [BioC] Experimental design for RNA-Seq   Tan, Yifang
• [BioC] help with annaffy package   Taylor, Katie
• [BioC] help with illumina microarray (DASL)   Taylor, Katie
• [BioC] help with annaffy package   Taylor, Katie
• [BioC] help with multtest and annaffy   Taylor, Katie
• [BioC] help with lumi   Taylor, Katie
• [BioC] annotating lumi   Taylor, Katie
• [BioC] Mapping NCBI accession numbers to GO terms   Steve Taylor
• [BioC] Affymetrix GeneChip Human Gene 1.0 ST Batch Effect and Saturation   Dennis Ting
• [BioC] Alignment viewer?   Joern Toedling
• [BioC] annotating reads acording with position on mapping   Joern Toedling
• [BioC] Openings in the Consulting Department of XLSolutions Corp   Sue Turner
• [BioC] Courses***More R courses scheduled for June 2010 by XLSolutions Corp   Sue Turner
• [BioC] Agilent arrays missing spots   Bjoern Usadel
• [BioC] Read single channel GenePix in limma [was: Analyze miRNA experiment in Bioconductor]   Vishnuvardhana, Ashwin [BSD] - SRF
• [BioC] Read single channel GenePix in limma [was: Analyze miRNA experiment in Bioconductor]   Vishnuvardhana, Ashwin [BSD] - SRF
• [BioC] R functions for genetic distances   Waddell, Peter J
• [BioC] Problem with createAnnObjs.HUMANCHIP_DB   Wendelin Waunzel
• [BioC] Mapping NCBI accession numbers to GO terms   January Weiner
• [BioC] SPIA package problem   January Weiner
• [BioC] What to do with this data? Question on deconfouding and GO analysis   January Weiner
• [BioC] ConsensusClusterPlus updated to 1.0.1   Matt Wilkerson
• [BioC] Alignment viewer?   Erik Wright
• [BioC] Alignment viewer?   Erik Wright
• [BioC] GEOquery, GSE, and MAList   Timothy Wu
• [BioC] GEOquery getGEO "error in scan"   Timothy Wu
• [BioC] Unable to get the Platform Table using fData on eset object   Sailu Yellaboina
• [BioC] GEO annotations   Assa Yeroslaviz
• [BioC] GEO annotations   Assa Yeroslaviz
• [BioC] GEO annotations   Assa Yeroslaviz
• [BioC] GEO annotations   Assa Yeroslaviz
• [BioC] How to show the definition of readFastq   Peng Yu
• [BioC] How to show the definition of readFastq   Peng Yu
• [BioC] Typo in ?FastqQuality help page?   Peng Yu
• [BioC] How to see XStringSet's definition?   Peng Yu
• [BioC] How to show the definition of readFastq   Peng Yu
• [BioC] loop over IRanges spaces   Yvan
• [BioC] batch effect   Yisong Zhen
• [BioC] Chippeakanno, maxgap =1000   Zhu, Julie
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Zhu, Julie
• [BioC] ChIPpeakAnno Critical Bug   Zhu, Julie
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Zhu, Julie
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Zhu, Julie
• [BioC] ChIPpeakAnno Critical Bug   Zhu, Julie
• [BioC] ChIPpeakAnno Strandedness and distance calculation   Zhu, Julie
• [BioC] ChIPpeakAnno: New Features: distance calculation based on user selection of location of the peak and location of feature   Zhu, Julie
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Zhu, Julie
• [BioC] [Bioc-devel] Problem with merge   Zhu, Julie
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Zhu, Julie
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Zhu, Julie
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Zhu, Julie
• [BioC] ChIPpeakAnno annotatePeakInBatch error message   Zhu, Julie
• [BioC] GenomeGraphs issue   Zoppoli, Gabriele (NIH/NCI) [G]
• [BioC] GEOquery error when parsing Agilent annotation (?)   axel.klenk at actelion.com
• [BioC] Validated miRNAs revisited   mauede at alice.it
• [BioC] R: Validated miRNAs revisited   mauede at alice.it
• [BioC] Help with the terminology   mauede at alice.it
• [BioC] Query ERROR: caught BioMart::Exception   mauede at alice.it
• [BioC] Follow-up -> ERROR: caught BioMart::Exception:   mauede at alice.it
• [BioC] Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   mauede at alice.it
• [BioC] R: Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   mauede at alice.it
• [BioC] R: R: Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs   mauede at alice.it
• [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   mauede at alice.it
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   mauede at alice.it
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   mauede at alice.it
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   mauede at alice.it
• [BioC] after updating biomaRt cannot connect any more   mauede at alice.it
• [BioC] is database RefSeq achievable from any Bioconductor package   mauede at alice.it
• [BioC] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?   mauede at alice.it
• [BioC] Using Limma for peptide array analysis - technical replicate issues and false positives   K.Z.Nambiar at bsms.ac.uk
• [BioC] package pair "hugene10stv1cdf"/"hugene10stprobeset.db"   cstrato
• [BioC] problem with xps and annotation file from affymetrix mirna array   cstrato
• [BioC] problem with xps and annotation file from affymetrix mirna array   cstrato
• [BioC] XPS: scheme file repository and other news   cstrato
• [BioC] Bioconductor Digest, Vol 87, Issue 2   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 17   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 25   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] Bioconductor Digest, Vol 87, Issue 10   avinash gupta
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   qin kuang
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   qin kuang
• [BioC] LIMMA: data with technical replicate/familial relationship/biological replicate   qin kuang
• [BioC] exon array Problem   l.mohammadikhankahdani
• [BioC] Error using getMeans function in Ringo/Starr   zacher at lmb.uni-muenchen.de
• [BioC] Perform merge analysis   sneha patil
• [BioC] RMA without probe summarization   sneha patil
• [BioC] Reading .bpmap files for homemade tiling arrays   raphaelgottardo
• [BioC] Saving/loading Genominator ExpData-class object   rcaloger
• [BioC] Saving/loading Genominator ExpData-class object   rcaloger
• [BioC] sir   deepak roshan
• [BioC] Reading in data with HTqPCR   deepak roshan
• [BioC] Query regarding Clustering   varpal singh
• [BioC] Query regarding Bioconductor   varpal singh
• [BioC] Query regarding for Entrez IDpackage   varpal singh
• [BioC] Query regarding entrez id   varpal singh
• [BioC] Thanks for solving problem related entrez id   varpal singh
• [BioC] Query regarding limma package   varpal singh
• [BioC] Query regarding contrast motrix   varpal singh
• [BioC] Rredland installation   anupam sinha
• [BioC] Rredland installation   anupam sinha
• [BioC] Hgu133acdf Installation Problem   mahalakshmi sivamani
• [BioC] Questions about using Limma   wei tie
• [BioC] Questions about using Limma   wei tie
• [BioC] question about CDF file   jchl tu
• [BioC] problem with xps and annotation file from affymetrix mirna array   giacomo.tuana at unimib.it
• [BioC] RGraphViz: length edges   prsmra01 at uniroma2.it
• [BioC] RGraphViz: length edges   prsmra01 at uniroma2.it
• [BioC] finding and deleting repeated observations   mervi.alanne at wri.fi
• [BioC] segfault with rmaMicroRna in AgiMicroRna package   heyi xiao
• [BioC] Aligned RNA-seq data to ranked list of genes   paulig2001 at yahoo.co.uk
• [BioC] computer out of memory when using sigpathway   山中程

Last message date: Mon May 31 23:47:18 CEST 2010
Archived on: Tue Jun 1 08:04:30 CEST 2010

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