August 2013 Archives by author

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Starting: Thu Aug 1 00:14:35 CEST 2013
Ending: Sat Aug 31 22:32:35 CEST 2013
Messages: 567

• [BioC] returning an objects GLCM using EBImage   David Stephens (Cefas)
• [BioC] Differential expression analysis in Limma for one factor after adjusting for a covariate   QAMRA Aditi (GIS)
• [BioC] basic query to make groups ..   ALok
• [BioC] A problem   tooba AbaC
• [BioC] Fst Calculation Packages   Ovokeraye Achinike-Oduaran
• [BioC] Fst Calculation Packages   Ovokeraye Achinike-Oduaran
• [BioC] [topGO] More flexible way to select 'interesting' genes   Adrian Alexa
• [BioC] SeqGSEA estiGeneNBstat()   Alleene
• [BioC] alignShortReads   Sonja Althammer
• [BioC] Problem reading Cel files - Oligo Package   Atul
• [BioC] Problem reading Cel files - Oligo Package   Atul
• [BioC] Annotating Results for HuEx 1.0 STv2 - Oligo   Atul
• [BioC] segfault ReadAffy cause 'memory not mapped'   Henrik Bengtsson
• [BioC] Rsamtools: sortBam() and 'samtools sort' does not give the same results   Henrik Bengtsson
• [BioC] Rsamtools: sortBam() and 'samtools sort' does not give the same results   Henrik Bengtsson
• [BioC] Problem reading Cel files - Oligo Package   Henrik Bengtsson
• [BioC] Problem reading Cel files - Oligo Package   Henrik Bengtsson
• [BioC] saving GRanges objects - resulting file size issue   Charles Berry
• [BioC] difference in results using different edgeR package versions   Fernando Biase
• [BioC] difference in results using different edgeR package versions   Fernando Biase
• [BioC] Connectionists: Open position for an Experienced Researcher at Johannes Kepler University Linz, Austria   Secretary Institute of Bioinformatics
• [BioC] IRanges::unlist in package   Blanchette, Marco
• [BioC] IRanges::unlist in package   Blanchette, Marco
• [BioC] IRanges::unlist in package   Blanchette, Marco
• [BioC] Bug in makeOrgPackageFromNCBI from AnnotationForge?   Blanchette, Marco
• [BioC] Bug in makeOrgPackageFromNCBI from AnnotationForge?   Blanchette, Marco
• [BioC] segfault ReadAffy cause 'memory not mapped'   Ben Bolstad
• [BioC] edgeR topTags output (logFC)   Susan Bush
• [BioC] AnnotationHub man page improvements   Vincent Carey
• [BioC] org.Mm.eg.db gives wrong symbol for MT genes   Vincent Carey
• [BioC] Phred encoding   Vincent Carey
• [BioC] AnnotationHub man page improvements   Marc Carlson
• [BioC] AnnotationHub man page improvements   Marc Carlson
• [BioC] AnnotationHub man page improvements   Marc Carlson
• [BioC] an error in AnnotationForge   Marc Carlson
• [BioC] Error in .testGOFrame(x, organism) and invalid GO Evidence codes   Marc Carlson
• [BioC] TranscriptDb of GENCODE Genes   Marc Carlson
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Marc Carlson
• [BioC] org.Mm.eg.db gives wrong symbol for MT genes   Marc Carlson
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Marc Carlson
• [BioC] I need BSgenome for Eucalyptus grandis   Marc Carlson
• [BioC] problem generating Chinese hamster txdb from GFF file   Marc Carlson
• [BioC] problem generating Chinese hamster txdb from GFF file   Marc Carlson
• [BioC] error of \"subscript out of bounds\" while applying basicProfile func   Marc Carlson
• [BioC] TxDb.Hsapiens.UCSC.hg19.knownGene: seqlevels() vs isActive()   Marc Carlson
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Marc Carlson
• [BioC] problem with makeOrgPackageFromNCBI (for Chinese hamster)   Marc Carlson
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Marc Carlson
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Marc Carlson
• [BioC] error while using goProfiles package on arabidopsis entrez gene IDs   Marc Carlson
• [BioC] Bug in makeOrgPackageFromNCBI from AnnotationForge?   Marc Carlson
• [BioC] Change enzyme code (EC) into gene symbol   Marc Carlson
• [BioC] segfault ReadAffy cause 'memory not mapped'   Benilton Carvalho
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Benilton Carvalho
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Robert Castelo
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Robert Castelo
• [BioC] DEseq for paired samples   Prabhakar Chalise
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Rameswara Sashi Kiran Challa
• [BioC] I need BSgenome for Eucalyptus grandis   Lukas Chavez
• [BioC] MEDIPS no longer producing AMS values   Lukas Chavez
• [BioC] MEDIPS, GRanges, IRanges error processing BAM file   Lukas Chavez
• [BioC] MEDIPS, GRanges, IRanges error processing BAM file   Lukas Chavez
• [BioC] SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays   Ying Chen
• [BioC] DESeq2 dependency hell   Mark Christie
• [BioC] Problem with RIPSeeker   Nicola Cole
• [BioC] Problem with RIPSeeker   Nicola Cole
• [BioC] GViz - successes and a few hopes   Cook, Malcolm
• [BioC] ggbio facet_gr example sought   Cook, Malcolm
• [BioC] ggbio facet_gr example sought   Cook, Malcolm
• [BioC] GViz - successes and a few hopes   Cook, Malcolm
• [BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor   Cook, Malcolm
• [BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor   Cook, Malcolm
• [BioC] Order within a GRanges object   Cook, Malcolm
• [BioC] Using precede()/follow() to find two ranges   Cook, Malcolm
• [BioC] Using precede()/follow() to find two ranges   Cook, Malcolm
• [BioC] Using precede()/follow() to find two ranges   Cook, Malcolm
• [BioC] Using precede()/follow() to find two ranges   Cook, Malcolm
• [BioC] Using precede()/follow() to find two ranges   Cook, Malcolm
• [BioC] [topGO] More flexible way to select 'interesting' genes   Kevin Coombes
• [BioC] Limma, model with several factors   Ingrid Dahlman
• [BioC] [devteam-bioc] Failure to update to Bioconductor 2.12 from bioconductor 2.11   Das, D.
• [BioC] RIPSeeker multicore option not working fully?   Davis, Wade
• [BioC] Opportunity at the Laboratory for Personalized Medicine with Harvard Medical School   Doe, Aimee
• [BioC] Problem with RIPSeeker   Antonio Domingues
• [BioC] HTqPCR problem with ttestCtData function   Ruben Dries
• [BioC] Semantics of GenomicRanges gaps()   Dan Du
• [BioC] import only partial samples of an array   Pan Du
• [BioC] topGO analysis returns different gene counts for category than given for non-model organism   Diana Toups Dugas
• [BioC] BiomaRt useMart() issues   Steffen Durinck
• [BioC] BiomaRt and archival versions of ensembl_mart   Steffen Durinck
• [BioC] using pathview about hsa01100   Ed
• [BioC] about running gsva on mac   Ed
• [BioC] MEDIPS no longer producing AMS values   Jonathan Ellis
• [BioC] MEDIPS no longer producing AMS values   Jonathan Ellis
• [BioC] MEDIPS, GRanges, IRanges error processing BAM file   Jonathan Ellis
• [BioC] MEDIPS, GRanges, IRanges error processing BAM file   Jonathan Ellis
• [BioC] minfi: control probes sequence   Rohmatul Fajriyah
• [BioC] minfi: control probes sequence   Rohmatul Fajriyah
• [BioC] minfi: control probes sequence   Rohmatul Fajriyah
• [BioC] minfi: control probes sequence   Rohmatul Fajriyah
• [BioC] ComBat: Error in FUN(newX[, i], ...) : (subscript) logical subscript too long   Farshad Farshidfar
• [BioC] [topGO] More flexible way to select 'interesting' genes   Enrico Ferrero
• [BioC] [topGO] More flexible way to select 'interesting' genes   Enrico Ferrero
• [BioC] [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?   Enrico Ferrero
• [BioC] [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?   Enrico Ferrero
• [BioC] [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?   Enrico Ferrero
• [BioC] mirDeep2 edgeR analysis   Flores Torres, Mariana
• [BioC] DESeq query   James Floyd
• [BioC] EdgeR: getting CPM values after batch effect correction   Gilgi Friedlander
• [BioC] Diffbind: Binding Affinity Heatmap   Giuseppe Gallone
• [BioC] Diffbind: Binding Affinity Heatmap   Giuseppe Gallone
• [BioC] error when loading mzR   Laurent Gatto
• [BioC] XCMS query regarding mzXML   Laurent Gatto
• [BioC] XCMS query regarding mzXML   Laurent Gatto
• [BioC] request   Laurent Gatto
• [BioC] Interpretation of output files   Julian Gehring
• [BioC] ggbio: Data stored twice in 'GGbio' object   Julian Gehring
• [BioC] ggbio: Data stored twice in 'GGbio' object   Julian Gehring
• [BioC] Depth of Coverage and Base counts from BAM file   Julian Gehring
• [BioC] GWASTools   Stephanie M. Gogarten
• [BioC] GWASTools   Stephanie M. Gogarten
• [BioC] how to do the time series analysis?   Wuming Gong
• [BioC] tweeDEseq main paper   Gonzalez Ruiz, Juan Ramon
• [BioC] tweeDEseq glm reduced model specification?   Gonzalez Ruiz, Juan Ramon
• [BioC] HTqPCR package   VETTER Guillaume
• [BioC] Hello, reading large Affymetrix microarrays .CEL files   Nehme Hachem
• [BioC] GViz - successes and a few hopes   Hahne, Florian
• [BioC] confusing P-value (from egdeR) of one gene   Xinwei Han
• [BioC] combining/merging several ExpressionSet objects from SCAN   Juliet Hannah
• [BioC] combining/merging several ExpressionSet objects from SCAN   Juliet Hannah
• [BioC] combining/merging several ExpressionSet objects from SCAN   Juliet Hannah
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Juliet Hannah
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Juliet Hannah
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Juliet Hannah
• [BioC] AnnotationHub man page improvements   Kasper Daniel Hansen
• [BioC] AnnotationHub man page improvements   Kasper Daniel Hansen
• [BioC] likely bug in cbind() for DataFrame   Kasper Daniel Hansen
• [BioC] likely bug in cbind() for DataFrame   Kasper Daniel Hansen
• [BioC] about running gsva on mac   Kasper Daniel Hansen
• [BioC] AnnotationHub man page improvements   Kasper Daniel Hansen
• [BioC] AnnotationHub man page improvements   Kasper Daniel Hansen
• [BioC] Filtering BAM files by start position for VariantTools   Kasper Daniel Hansen
• [BioC] segfault ReadAffy cause 'memory not mapped'   Kasper Daniel Hansen
• [BioC] combining/merging several ExpressionSet objects from SCAN   Kasper Daniel Hansen
• [BioC] combining/merging several ExpressionSet objects from SCAN   Kasper Daniel Hansen
• [BioC] 回复: Re: fRMA package   Hanyine
• [BioC] matchTable for pairwiseAlignment in Biostrings?   Brian Herb
• [BioC] matchTable for pairwiseAlignment in Biostrings?   Brian Herb
• [BioC] Limma\'s roast() does not accept weigths in combination with block   Moritz Hess
• [BioC] Proper set up to test interaction of continuous covariate and factor levels (limma)   Moritz Hess
• [BioC] Proper set up to test interaction of continuous covariate and factor levels (limma)   Moritz Hess
• [BioC] findOverlaps() fails with type = 'equal' fails when query is a CollapsedVCF object and subject is a GRanges object   Peter Hickey
• [BioC] Measuring shifts in intronic expression independently of exons   Aliaksei Holik
• [BioC] problem generating Chinese hamster txdb from GFF file   Hooiveld, Guido
• [BioC] problem generating Chinese hamster txdb from GFF file   Hooiveld, Guido
• [BioC] problem generating Chinese hamster txdb from GFF file   Hooiveld, Guido
• [BioC] problem with makeOrgPackageFromNCBI (for Chinese hamster)   Hooiveld, Guido
• [BioC] problem with makeOrgPackageFromNCBI (for Chinese hamster)   Hooiveld, Guido
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Hooiveld, Guido
• [BioC] request   Wolfgang Huber
• [BioC] request   Wolfgang Huber
• [BioC] Measuring shifts in intronic expression independently of exons   Wolfgang Huber
• [BioC] Unable to find an inherited method for function ‘exprs’   Wolfgang Huber
• [BioC] Unable to find an inherited method for function ‘exprs’   Wolfgang Huber
• [BioC] frma normalization and batch effects   Wolfgang Huber
• [BioC] Measuring shifts in intronic expression independently of exons   Wolfgang Huber
• [BioC] cdf redesign   Claudio Isella
• [BioC] saving GRanges objects - resulting file size issue   Andrew Jaffe
• [BioC] TxDb.Hsapiens.UCSC.hg19.knownGene: seqlevels() vs isActive()   Andrew Jaffe
• [BioC] test for overlap   Adrian Johnson
• [BioC] ComBat: Could it utilize technical replicates?   Johnson, William Evan
• [BioC] combining/merging several ExpressionSet objects from SCAN   Johnson, William Evan
• [BioC] ComBat: Could it utilize technical replicates?   Johnson, William Evan
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   Johnson, William Evan
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   Johnson, William Evan
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   Johnson, William Evan
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   Johnson, William Evan
• [BioC] Bioconductor: CPM and log(CPM) values in EdgeR does not match   CSRK (Christian Schrøder Kaas)
• [BioC] Job: Bioinformatician (m/f) Core Facility - Mainz, Germany   Holger Klein
• [BioC] ComBat: Could it utilize technical replicates?   Essi Laajala
• [BioC] ComBat: Could it utilize technical replicates?   Essi Laajala
• [BioC] *Ranges paper published   Peter Langfelder
• [BioC] microarray outlier detection   Peter Langfelder
• [BioC] Error converting SBML to graph Object using R SBML   Michael Lawrence
• [BioC] likely bug in cbind() for DataFrame   Michael Lawrence
• [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
• [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
• [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
• [BioC] likely bug in cbind() for DataFrame   Michael Lawrence
• [BioC] ggbio: Data stored twice in 'GGbio' object   Michael Lawrence
• [BioC] ggbio facet_gr example sought   Michael Lawrence
• [BioC] Extracting overlapping gene names from a list of peaks   Michael Lawrence
• [BioC] GenomicRanges::reduce feature request   Michael Lawrence
• [BioC] *Ranges paper published   Michael Lawrence
• [BioC] Reopening of Computational Biologist position at Genentech   Michael Lawrence
• [BioC] merge on DataFrame forcing character->factor   Michael Lawrence
• [BioC] Job in GWAS / Next Gen Sequencing / genetics   Paul Leo
• [BioC] error when loading mzR   Steve Lianoglou
• [BioC] difference in results using different edgeR package versions   Steve Lianoglou
• [BioC] request   Steve Lianoglou
• [BioC] GenomicRanges::reduce feature request   Steve Lianoglou
• [BioC] Gviz ideogram error   Steve Lianoglou
• [BioC] Problem with RIPSeeker   Steve Lianoglou
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Steve Lianoglou
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Steve Lianoglou
• [BioC] Using precede()/follow() to find two ranges   Steve Lianoglou
• [BioC] Hello, reading large Affymetrix microarrays .CEL files   Steve Lianoglou
• [BioC] Finding my un-counted reads   Steve Lianoglou
• [BioC] Finding my un-counted reads   Steve Lianoglou
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Yang Liao
• [BioC] PhD position in Epigenetic mechanisms Bioinformatics and Modeling- University of Cambridge   Pietro Lio'
• [BioC] inSilicoMerging package   Li Liu
• [BioC] fRMA package   Li Liu
• [BioC] fRMA package   Li Liu
• [BioC] fRMA package   Li Liu
• [BioC] FW: fRMA package   Li Liu
• [BioC] DWD method for batch effect removal   Li Liu
• [BioC] DWD method for batch effect removal   Li Liu
• [BioC] DWD method for batch effect removal   Li Liu
• [BioC] FW: DWD method for batch effect removal   Li Liu
• [BioC] Mapping Affymetrix annotations with Bioconductor annotations   Joao Sollari Lopes
• [BioC] Mapping Affymetrix annotations with Bioconductor annotations   Joao Sollari Lopes
• [BioC] Mapping Affymetrix annotations with Bioconductor annotations   Joao Sollari Lopes
• [BioC] segfault ReadAffy cause 'memory not mapped'   Loraine, Ann
• [BioC] DESeq query   Michael Love
• [BioC] Using the genes.count-tracking file from cuffdiff in DESeq   Michael Love
• [BioC] DEseq for paired samples   Michael Love
• [BioC] cdf redesign   James W. MacDonald
• [BioC] Failure to update to Bioconductor 2.12 from bioconductor 2.11   James W. MacDonald
• [BioC] Limma: how to set the selection by p-value   James W. MacDonald
• [BioC] Extracting overlapping gene names from a list of peaks   James W. MacDonald
• [BioC] IRanges::unlist in package   James W. MacDonald
• [BioC] Can logFC be used to determine effect size?   James W. MacDonald
• [BioC] take the average log fc for each gene   James W. MacDonald
• [BioC] take the average log fc for each gene   James W. MacDonald
• [BioC] Affy: probeset to gene expression with expresso   James W. MacDonald
• [BioC] Affy: probeset to gene expression with expresso   James W. MacDonald
• [BioC] Affy: probeset to gene expression with expresso   James W. MacDonald
• [BioC] DESeq2 dependency hell   James W. MacDonald
• [BioC] Limma, model with several factors   James W. MacDonald
• [BioC] RMA probe summarization when sizes of probesets are unequal   James W. MacDonald
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   James W. MacDonald
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   James W. MacDonald
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   James W. MacDonald
• [BioC] Proper set up to test interaction of continuous covariate and factor levels (limma)   James W. MacDonald
• [BioC] Problem reading Cel files - Oligo Package   James W. MacDonald
• [BioC] Mapping Affymetrix annotations with Bioconductor annotations   James W. MacDonald
• [BioC] Mapping Affymetrix annotations with Bioconductor annotations   James W. MacDonald
• [BioC] Differential expression analysis in Limma for one factor after adjusting for a covariate   James W. MacDonald
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Aaron Mackey
• [BioC] Control probe QC plots for Infinium 450k chips (lumi, minfi...)   Jon Manning
• [BioC] segfault ReadAffy cause 'memory not mapped'   Matthew McCall
• [BioC] segfault ReadAffy cause 'memory not mapped'   Matthew McCall
• [BioC] frma normalization and batch effects   Matthew McCall
• [BioC] Finding my un-counted reads   Sam McInturf
• [BioC] Finding my un-counted reads   Sam McInturf
• [BioC] Problems with 'dataset' argument for parseWorkspace() or read.flowSet()   Mike
• [BioC] Filtering BAM files by start position for VariantTools   Martin Morgan
• [BioC] segfault ReadAffy cause 'memory not mapped'   Martin Morgan
• [BioC] Gviz ideogram error   Martin Morgan
• [BioC] combining/merging several ExpressionSet objects from SCAN   Martin Morgan
• [BioC] combining/merging several ExpressionSet objects from SCAN   Martin Morgan
• [BioC] Matrix package bug?   Martin Morgan
• [BioC] I need BSgenome for Eucalyptus grandis   Martin Morgan
• [BioC] Phred encoding   Martin Morgan
• [BioC] Annotate blastSequences Returns No Result   Martin Morgan
• [BioC] Annotate blastSequences Returns No Result   Martin Morgan
• [BioC] Bioconductor Job Opportunities   Martin Morgan
• [BioC] A problem   Martin Morgan
• [BioC] alignShortReads   Martin Morgan
• [BioC] Using precede()/follow() to find two ranges   Martin Morgan
• [BioC] Rsamtools: sortBam() and 'samtools sort' does not give the same results   Martin Morgan
• [BioC] Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle   Martin Morgan
• [BioC] Genes, their domains, and a list of superimposed mutations   Martin Morgan
• [BioC] Measuring shifts in intronic expression independently of exons   Martin Morgan
• [BioC] request   Alexey Moskalev
• [BioC] request   Alexey Moskalev
• [BioC] request   Alexey Moskalev
• [BioC] pathview puzzle   Oleg Moskvin
• [BioC] pathview puzzle   Oleg Moskvin
• [BioC] Matrix package bug?   Mueller, Arne
• [BioC] SKAT package on CRAN   Cian Murphy
• [BioC] Chr Info for array CGH - agilent 60K   Cian Murphy
• [BioC] EdgeR: general advice on using edgeR for sRNA analysis   Kenlee Nakasugi
• [BioC] EdgeR: general advice on using edgeR for sRNA analysis   Kenlee Nakasugi
• [BioC] EdgeR: sRNA analysis check   Kenlee Nakasugi
• [BioC] Pathview for global and overview maps Re: using pathview about hsa01100   Nick
• [BioC] Pathview for global and overview maps Re: using pathview about hsa01100   Nick
• [BioC] Change enzyme code (EC) into gene symbol   Nick
• [BioC] Change enzyme code (EC) into gene symbol   Nick
• [BioC] Change enzyme code (EC) into gene symbol   Nick
• [BioC] Change enzyme code (EC) into gene symbol   Nick
• [BioC] Order within a GRanges object   Hermann Norpois
• [BioC] RNASeq:- getting Zero Count   Valerie Obenchain
• [BioC] RNASeq:- getting Zero Count   Valerie Obenchain
• [BioC] RNASeq:- getting Zero Count   Valerie Obenchain
• [BioC] saving GRanges objects - resulting file size issue   Valerie Obenchain
• [BioC] saving GRanges objects - resulting file size issue   Valerie Obenchain
• [BioC] [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?   Valerie Obenchain
• [BioC] [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?   Valerie Obenchain
• [BioC] matchTable for pairwiseAlignment in Biostrings?   Valerie Obenchain
• [BioC] Semantics of GenomicRanges gaps()   Valerie Obenchain
• [BioC] findOverlaps() fails with type = 'equal' fails when query is a CollapsedVCF object and subject is a GRanges object   Valerie Obenchain
• [BioC] Finding my un-counted reads   Valerie Obenchain
• [BioC] Finding my un-counted reads   Valerie Obenchain
• [BioC] matchTable for pairwiseAlignment in Biostrings?   Valerie Obenchain
• [BioC] topGO analysis returns different gene counts for category than given for non-model organism   Valerie Obenchain
• [BioC] R package cleanUpdTSeq   Ou, Jianhong
• [BioC] IRanges::unlist in package   Hervé Pagès
• [BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor   Hervé Pagès
• [BioC] BUG? when setting mcols of a GRanges to a DataFrame one of whose columns is an ordered factor   Hervé Pagès
• [BioC] I need BSgenome for Eucalyptus grandis   Hervé Pagès
• [BioC] Order within a GRanges object   Hervé Pagès
• [BioC] returning an objects GLCM using EBImage   Gregoire Pau
• [BioC] Measuring shifts in intronic expression independently of exons   James Perkins
• [BioC] Measuring shifts in intronic expression independently of exons   James Perkins
• [BioC] how to do the time series analysis?   Wang Peter
• [BioC] how to do the time series analysis?   Wang Peter
• [BioC] Fwd: ComBat_ Error in solve.default(t(design) %*% design) : Lapack routine dgesv: system is exactly singular   Dr J. Peters
• [BioC] matchPWM   Massimo Petretich
• [BioC] segfault ReadAffy cause 'memory not mapped'   Brian D. Peyser PhD
• [BioC] segfault ReadAffy cause 'memory not mapped'   Brian D. Peyser PhD
• [BioC] segfault ReadAffy cause 'memory not mapped'   Brian D. Peyser PhD
• [BioC] segfault ReadAffy cause 'memory not mapped'   Brian D. Peyser PhD
• [BioC] segfault ReadAffy cause 'memory not mapped'   Brian D. Peyser PhD
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Sarah Pohl
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Sarah Pohl
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria   Sarah Pohl
• [BioC] Affy: probeset to gene expression with expresso   Martin Preusse
• [BioC] Affy: probeset to gene expression with expresso   Martin Preusse
• [BioC] Affy: probeset to gene expression with expresso   Martin Preusse
• [BioC] Affy: probeset to gene expression with expresso   Martin Preusse
• [BioC] Affy: probeset to gene expression with expresso   Martin Preusse
• [BioC] segfault ReadAffy cause 'memory not mapped'   Adaikalavan Ramasamy
• [BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   Martin Rijlaarsdam
• [BioC] Bioconductor: CPM and log(CPM) values in EdgeR does not match   Mark Robinson
• [BioC] GenomeStudio output and lumi   Sanja Rogic
• [BioC] tweeDEseq glm reduced model specification?   Ryan
• [BioC] EdgeR: getting CPM values after batch effect correction   Ryan
• [BioC] about running gsva on mac   Devon Ryan
• [BioC] basic query to make groups ..   Devon Ryan
• [BioC] DEseq for paired samples   Devon Ryan
• [BioC] microarray outlier detection   Devon Ryan
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Sashi
• [BioC] defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package   Sashi
• [BioC] Extracting overlapping gene names from a list of peaks   Patrick Schorderet
• [BioC] Gviz ideogram error   Siddharth Sethi
• [BioC] [devteam-bioc] Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library   Paul Shannon
• [BioC] [devteam-bioc] Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library   Paul Shannon
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts   Wei Shi
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Wei Shi
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Wei Shi
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Wei Shi
• [BioC] Reading Illumina data from GenomeStudio in limma   Wei Shi
• [BioC] Reading Illumina data from GenomeStudio in limma   Wei Shi
• [BioC] RNASeq:- getting Zero Count   Reema Singh
• [BioC] RNASeq:- getting Zero Count   Reema Singh
• [BioC] XCMS query regarding mzXML   Reema Singh
• [BioC] XCMS query regarding mzXML   Reema Singh
• [BioC] RNASeq:- getting Zero Count   Reema Singh
• [BioC] RNASeq:- getting Zero Count   Reema Singh
• [BioC] BiomaRt and archival versions of ensembl_mart   Greg Slodkowicz
• [BioC] BiomaRt and archival versions of ensembl_mart   Greg Slodkowicz
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts   Alan Smith
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Alan Smith
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Alan Smith
• [BioC] Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis   Alan Smith
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Alan Smith
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Alan Smith
• [BioC] Gene Vs Transcript level Differential expression analysis   Alan Smith
• [BioC] take the average log fc for each gene   Helen Smith
• [BioC] Affy: probeset to gene expression with expresso   Helen Smith
• [BioC] beadarray library: perBeadFile   Mike Smith
• [BioC] EdgeR: general advice on using edgeR for sRNA analysis   Gordon K Smyth
• [BioC] Limma\'s roast() does not accept weigths in combination with block   Gordon K Smyth
• [BioC] Limma, model with several factors   Gordon K Smyth
• [BioC] Can logFC be used to determine effect size?   Gordon K Smyth
• [BioC] org.Mm.eg.db gives wrong symbol for MT genes   Gordon K Smyth
• [BioC] org.Mm.eg.db gives wrong symbol for MT genes   Gordon K Smyth
• [BioC] EdgeR: sRNA analysis check   Gordon K Smyth
• [BioC] EdgeR annotation   Gordon K Smyth
• [BioC] Complex Limma design: technical replication, biological replication and repeated experiment   Gordon K Smyth
• [BioC] edgeR topTags output (logFC)   Gordon K Smyth
• [BioC] edgeR topTags output (logFC)   Gordon K Smyth
• [BioC] confusing P-value of one gene   Gordon K Smyth
• [BioC] EdgeR   Gordon K Smyth
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Gordon K Smyth
• [BioC] predFC doesn't use norm factors?   Gordon K Smyth
• [BioC] relations package   Nikul Soni
• [BioC] cummeRbund installation Error   Sridhar Srinivasan
• [BioC] Bioconductor: CPM and log(CPM) values in EdgeR does not match   Michael Stadler
• [BioC] Diffbind: Binding Affinity Heatmap   Rory Stark
• [BioC] Diffbind: Binding Affinity Heatmap   Rory Stark
• [BioC] DiffBind - Dropbox containing vignette data   Rory Stark
• [BioC] DiffBind questions   Rory Stark
• [BioC] 'version' is missing error when running makeTxDbPackageFromUCSC   Michael Steeves
• [BioC] 'version' is missing error when running makeTxDbPackageFromUCSC   Michael Steeves
• [BioC] TranscriptDb of GENCODE Genes   Dario Strbenac
• [BioC] Problem with importing bigWig file from GEO with rtracklayer?   Dario Strbenac
• [BioC] Annotate blastSequences Returns No Result   Dario Strbenac
• [BioC] Annotate blastSequences Returns No Result   Dario Strbenac
• [BioC] RankProd Result for One Class Analysis   Dario Strbenac
• [BioC] bioMart GO inconsistency, normal?   R Tagett
• [BioC] Unable to find an inherited method for function ‘exprs’   Dave Tang
• [BioC] Unable to find an inherited method for function ‘exprs’   Dave Tang
• [BioC] Unable to find an inherited method for function ‘exprs’   Dave Tang
• [BioC] merge on DataFrame forcing character->factor   Murat Tasan
• [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
• [BioC] DNAStringSetList can't coerce a list?   Taylor, Sean D
• [BioC] DNAStringSetList can't coerce a list?   Taylor, Sean D
• [BioC] DNAStringSetList can't coerce a list?   Taylor, Sean D
• [BioC] Phred encoding   Taylor, Sean D
• [BioC] Phred encoding   Taylor, Sean D
• [BioC] Phred encoding   Taylor, Sean D
• [BioC] error when loading mzR   Dan Tenenbaum
• [BioC] error when loading mzR   Dan Tenenbaum
• [BioC] about running gsva on mac   Dan Tenenbaum
• [BioC] inSilicoMerging package   Dan Tenenbaum
• [BioC] Filtering BAM files by start position for VariantTools   Dan Tenenbaum
• [BioC] AnnotationHub man page improvements   Dan Tenenbaum
• [BioC] AnnotationHub man page improvements   Dan Tenenbaum
• [BioC] Filtering BAM files by start position for VariantTools   Dan Tenenbaum
• [BioC] [devteam-bioc] Failure to update to Bioconductor 2.12 from bioconductor 2.11   Dan Tenenbaum
• [BioC] fRMA package   Dan Tenenbaum
• [BioC] fRMA package   Dan Tenenbaum
• [BioC] fRMA package   Dan Tenenbaum
• [BioC] fRMA package   Dan Tenenbaum
• [BioC] DWD method for batch effect removal   Dan Tenenbaum
• [BioC] DWD method for batch effect removal   Dan Tenenbaum
• [BioC] DWD method for batch effect removal   Dan Tenenbaum
• [BioC] DWD method for batch effect removal   Dan Tenenbaum
• [BioC] FW: DWD method for batch effect removal   Dan Tenenbaum
• [BioC] cummeRbund installation Error   Dan Tenenbaum
• [BioC] SKAT package on CRAN   Dan Tenenbaum
• [BioC] relations package   Dan Tenenbaum
• [BioC] SeqGSEA estiGeneNBstat()   Dan Tenenbaum
• [BioC] HTqPCR normalization issue ?   Dan Tenenbaum
• [BioC] 'version' is missing error when running makeTxDbPackageFromUCSC   Dan Tenenbaum
• [BioC] download packages VariantTools   Dan Tenenbaum
• [BioC] download packages VariantTools   Dan Tenenbaum
• [BioC] download packages VariantTools   Dan Tenenbaum
• [BioC] download packages VariantTools   Dan Tenenbaum
• [BioC] combining/merging several ExpressionSet objects from SCAN   Ryan C. Thompson
• [BioC] edgeR v2.6 vs. v3.2.4   Ryan C. Thompson
• [BioC] mirDeep2 edgeR analysis   Ryan C. Thompson
• [BioC] TCC RNAseq normalization package error   Ryan C. Thompson
• [BioC] EdgeR: getting CPM values after batch effect correction   Ryan C. Thompson
• [BioC] EdgeR: getting CPM values after batch effect correction   Ryan C. Thompson
• [BioC] Filtering BAM files by start position for VariantTools   Tim Triche, Jr.
• [BioC] combining/merging several ExpressionSet objects from SCAN   Tim Triche, Jr.
• [BioC] [Bioc-devel] *Ranges paper published   Tim Triche, Jr.
• [BioC] combining/merging several ExpressionSet objects from SCAN   Tim Triche, Jr.
• [BioC] combining/merging several ExpressionSet objects from SCAN   Tim Triche, Jr.
• [BioC] combining/merging several ExpressionSet objects from SCAN   Tim Triche, Jr.
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Tim Triche, Jr.
• [BioC] RSEM for transcript and gene level read count and edgeR differential expression analysis   Tim Triche, Jr.
• [BioC] Control probe QC plots for Infinium 450k chips (lumi, minfi...)   Tim Triche, Jr.
• [BioC] minfi: control probes sequence   Tim Triche, Jr.
• [BioC] minfi: control probes sequence   Tim Triche, Jr.
• [BioC] minfi: control probes sequence   Tim Triche, Jr.
• [BioC] error when loading mzR   Monika Tokmina-Lukaszewska
• [BioC] error when loading mzR   Monika Tokmina-Lukaszewska
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Nitesh Turaga
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Nitesh Turaga
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Nitesh Turaga
• [BioC] beadarray library: perBeadFile   Nogales Vilardell
• [BioC] relations package   Leif Väremo
• [BioC] [topGO] More flexible way to select 'interesting' genes   Levi Waldron
• [BioC] topGO question   Datong Wang
• [BioC] SeqGSEA estiGeneNBstat()   Xi Wang
• [BioC] Pathview with non-KEGG organisms?   Luo Weijun
• [BioC] using pathview about hsa01100   Luo Weijun
• [BioC] pathview, when multiple entrzgene ids were mapper to the same node in kegg pathway   Luo Weijun
• [BioC] Pathview for global and overview maps Re: using pathview about hsa01100   Luo Weijun
• [BioC] Pathview for global and overview maps Re: using pathview about hsa01100   Luo Weijun
• [BioC] Pathview for global and overview maps Re: using pathview about hsa01100   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] enrichment packages that accept t-stat (or related stat) as input   Luo Weijun
• [BioC] Change enzyme code (EC) into gene symbol   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] Problem with importing bigWig file from GEO with rtracklayer?   Hollis Wright
• [BioC] ggbio facet_gr example sought   Tengfei Yin
• [BioC] rtracklayer problem on large number of GRanges   Janet Young
• [BioC] NAs as result for enrichPathway   Yu, Guangchuang
• [BioC] Error in .testGOFrame(x, organism) and invalid GO Evidence codes   Zhidong Yuan
• [BioC] Problems with 'dataset' argument for parseWorkspace() or read.flowSet()   Silke Zachariae
• [BioC] Limma, model with several factors   Zadeh, Jenny Drnevich
• [BioC] Limma, model with several factors   Zadeh, Jenny Drnevich
• [BioC] predFC doesn't use norm factors?   Zadeh, Jenny Drnevich
• [BioC] FW: Computational biology position   Zhang,Jianhua
• [BioC] GenomicRanges::reduce feature request   Zhu, Lihua (Julie)
• [BioC] GenomicRanges::reduce feature request   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno-makeVennDiagram question   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno-makeVennDiagram question   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno-makeVennDiagram question   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno::assignChromosomeRegion   Zhu, Lihua (Julie)
• [BioC] question on ChIPpeakAnno::getEnrichedGO   Zhu, Lihua (Julie)
• [BioC] Interpretation of output files   from a TSSi user [guest]
• [BioC] Rankprod- gene appearing in both up and down regulated lists?   Adam Cornwell [guest]
• [BioC] Using the genes.count-tracking file from cuffdiff in DESeq   Alejandro [guest]
• [BioC] HTqPCR normalization issue ?   Alessandro Guffanti [guest]
• [BioC] TCC RNAseq normalization package error   Asela Wijeratne [guest]
• [BioC] CGHCall problems   Bernard North [guest]
• [BioC] Depth of Coverage and Base counts from BAM file   Chandu [guest]
• [BioC] import only partial samples of an array   Chris [guest]
• [BioC] Failure to update to Bioconductor 2.12 from bioconductor 2.11   Debatosh Das [guest]
• [BioC] Genes, their domains, and a list of superimposed mutations   Gabriele [guest]
• [BioC] Can logFC be used to determine effect size?   Jack [guest]
• [BioC] Complex Limma design: technical replication, biological replication and repeated experiment   Jana [guest]
• [BioC] Reading Illumina data from GenomeStudio in limma   Josh [guest]
• [BioC] frma normalization and batch effects   Judith Boer [guest]
• [BioC] DESeq2 dependency hell   Mark Christie [guest]
• [BioC] error when loading mzR   Monika Lukaszewska [guest]
• [BioC] Limma\'s roast() does not accept weigths in combination with block   Moritz Hess [guest]
• [BioC] Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library   Nicole A Thompson [guest]
• [BioC] edgeR annotation mission from topTags output   R [guest]
• [BioC] beadarray\'s processSwathData for HumanHT12v4, with 3 swaths   Rebecca Tagett [guest]
• [BioC] I need BSgenome for Eucalyptus grandis   Rodrigo Hasbun [guest]
• [BioC] Package/Function for Single Channel Microarray Spatial Normalization?   Scott Robinson [guest]
• [BioC] Can I input ordinal variables into a model in Limma?   Scott Robinson [guest]
• [BioC] edgeR topTags output (logFC)   Susan [guest]
• [BioC] RMA probe summarization when sizes of probesets are unequal   Xin Lin [guest]
• [BioC] error of \"subscript out of bounds\" while applying basicProfile func   d [guest]
• [BioC] NAs as result for enrichPathway   dd [guest]
• [BioC] error while using goProfiles package on arabidopsis entrez gene IDs   dd [guest]
• [BioC] Limma: how to set the selection by p-value   guest [guest]
• [BioC] microarray outlier detection   guest [guest]
• [BioC] question about package AgiMicroRna   maryam shahmansouri [guest]
• [BioC] edgeR v2.6 vs. v3.2.4   mwheeler [guest]
• [BioC] XPS package QC data   b a
• [BioC] XPS package QC data   b a
• [BioC] download packages VariantTools   francesca bergantino
• [BioC] download packages VariantTools   francesca bergantino
• [BioC] download packages VariantTools   francesca bergantino
• [BioC] edgeR   Joanne.Lee at csiro.au
• [BioC] segfault ReadAffy cause 'memory not mapped'   cstrato
• [BioC] XPS package QC data   cstrato
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   cstrato
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   cstrato
• [BioC] segfault ReadAffy cause 'memory not mapped'   cstrato
• [BioC] XPS package QC data   cstrato
• [BioC] XPS package QC data   cstrato
• [BioC] XPS package QC data   cstrato
• [BioC] Error while background correction   kunal jha
• [BioC] an error in AnnotationForge   joseph
• [BioC] 答复: an error in AnnotationForge   joseph
• [BioC] 答复: an error in AnnotationForge   joseph
• [BioC] topgo GO mapping for non model organisms   km
• [BioC] BiomaRt useMart() issues   burak kutlu
• [BioC] BiomaRt useMart() issues   burak kutlu
• [BioC] Using precede()/follow() to find two ranges   d r
• [BioC] Using precede()/follow() to find two ranges   d r
• [BioC] Using precede()/follow() to find two ranges   d r
• [BioC] Using precede()/follow() to find two ranges   d r
• [BioC] ComBat_ Error in solve.default(t(design) %*% design) : Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] Fwd: ComBat_ Error in solve.default(t(design) %*% design) : Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0   amit kumar subudhi
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   heyi xiao
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   heyi xiao
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   heyi xiao
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   heyi xiao
• [BioC] RNA degradation plot with oligo package GeneFeatureSet objects   heyi xiao

Last message date: Sat Aug 31 22:32:35 CEST 2013
Archived on: Sat Aug 31 22:32:52 CEST 2013

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