September 2013 Archives by author

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Starting: Sun Sep 1 02:51:47 CEST 2013
Ending: Mon Sep 30 21:40:54 CEST 2013
Messages: 502

• [BioC] Differential expression analysis in Limma for one factor after adjusting for a covariate   QAMRA Aditi (GIS)
• [BioC] RLE plot from expression dataset   QAMRA Aditi (GIS)
• [BioC] SnpStats - STRING_ELT() error and Fst   Ovokeraye Achinike-Oduaran
• [BioC] snpStats Fst Implementation   Ovokeraye Achinike-Oduaran
• [BioC] topGO analysis returns different gene counts for category than given for non-model organism   Adrian Alexa
• [BioC] Unusual results with DESeq ?   Simon Anders
• [BioC] Getting Introns Expression at a Per Gene Level   Carl Baribault
• [BioC] problem while loading affycoretools   Henrik Bengtsson
• [BioC] coverage() in IRanges gives >0 coverage when weight == 0   Charles Berry
• [BioC] bug in GenomicRanges gaps?   Blanchette, Marco
• [BioC] bug in GenomicRanges gaps?   Blanchette, Marco
• [BioC] bug in GenomicRanges gaps?   Blanchette, Marco
• [BioC] Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions   Stuart Bradley
• [BioC] metagenomeSeq paper out in Nature Methods   Hector Corrada Bravo
• [BioC] DiffBind -error with dba.counts   Gordon Brown
• [BioC] DiffBind -error with dba.counts   Gordon Brown
• [BioC] DiffBind -error with dba.counts   Gordon Brown
• [BioC] Affymetrix HTA 2 array analysis   Vincent Carey
• [BioC] Boston Bioconductor Basics, Oct 10-11 2013   Vincent Carey
• [BioC] Course offering: Boston Bioconductor Basics, Oct 10-11 2013: Tuition cut for early registration   Vincent Carey
• [BioC] package availability for R3.01   Marc Carlson
• [BioC] package availability for R3.01   Marc Carlson
• [BioC] Simple pathway enrichment analysis for gene lists   Marc Carlson
• [BioC] problem with creating array annotation package   Marc Carlson
• [BioC] Error using makeDBPackage() from AnnotationForge package   Marc Carlson
• [BioC] topGO issues   Marc Carlson
• [BioC] problem with TXNAME -> SYMBOL mapping in Homo.sapiens library   Marc Carlson
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Benilton Carvalho
• [BioC] Affy HTA 2.0 array analysis   Benilton Carvalho
• [BioC] MEDIPS saturation error   Sara Castelletti
• [BioC] GSVA questions   Robert Castelo
• [BioC] replace nucleotide at fixed position in a DNAStringSet object   Robert Castelo
• [BioC] replace nucleotide at fixed position in a DNAStringSet object   Robert Castelo
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Robert Castelo
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Robert Castelo
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Robert Castelo
• [BioC] GOstats code validation   kaushal Raj Chaudhary
• [BioC] Which package I should use   Pet Chiang
• [BioC] How to deal with Affymetrix probe that map to multiple genes   Mete Civelek
• [BioC] Rsubread for paired end SOLID sequencing   Simon Coetzee
• [BioC] Remove batch effects from RNA-seq data using edgeR and sva/ComBat   Christopher Conley
• [BioC] BUG: median(IRanges::Rle(NA),na.rm=TRUE)) should return NA   Cook, Malcolm
• [BioC] BUG: median(IRanges::Rle(NA), na.rm=TRUE)) should return NA   Cook, Malcolm
• [BioC] bug in GenomicRanges gaps?   Cook, Malcolm
• [BioC] bug in GenomicRanges gaps?   Cook, Malcolm
• [BioC] Affymetrix HTA 2 array analysis   Mark Cowley
• [BioC] Affymetrix HTA 2 array analysis   Mark Cowley
• [BioC] ChIPpeakAnno, getAnnotation question   Neha Daga
• [BioC] Exception thrown in ReadAffy() when reading Hu-133B files in a GEO Dataset   Sean Davis
• [BioC] Regression Analysis   Sean Davis
• [BioC] getBM returns shorter vectors than values   Sean Davis
• [BioC] Biostrings::matchPattern,extract sequences   Marcus Davy
• [BioC] writeFastq to gzip compressed files   Marcus Davy
• [BioC] writeFastq to gzip compressed files   Marcus Davy
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Nicolas Delhomme
• [BioC] eayRNASeq with Ensemble GRCh37 help   Nicolas Delhomme
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Nicolas Delhomme
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Nicolas Delhomme
• [BioC] pathview puzzle   Pj Dias
• [BioC] Genes and Metabolites   Pj Dias
• [BioC] package availability for R3.01   Diego Diez
• [BioC] aCGH telling me to run find.hmm.states before merge hmm.states even though I have.   Dan Du
• [BioC] Horizontal text in Gviz title panel.   Dan Du
• [BioC] Horizontal text in Gviz title panel.   Dan Du
• [BioC] installation packages   Dan Du
• [BioC] topGO analysis returns different gene counts for category than given for non-model organism   Diana Toups Dugas
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   Mark Dunning
• [BioC] getBM returns shorter vectors than values   Steffen Durinck
• [BioC] longitudinal GWAS analysis   Joao Fadista
• [BioC] Simple pathway enrichment analysis for gene lists   Enrico Ferrero
• [BioC] Simple pathway enrichment analysis for gene lists   Enrico Ferrero
• [BioC] Simple pathway enrichment analysis for gene lists   Enrico Ferrero
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Felix Frey
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Felix Frey
• [BioC] cycle package question   Matthias Futschik
• [BioC] MakeDBPackage fails with SQL error   Gabriel
• [BioC] metabolomics data analysis   Laurent Gatto
• [BioC] Error: package \'mzR\' could not be loaded   Laurent Gatto
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Julian Gehring
• [BioC] Bioinformatics Facility Director Position at UC Riverside   Thomas Girke
• [BioC] readGAlignmentPairs error   Leonard Goldstein
• [BioC] readGAlignmentPairs error   Leonard Goldstein
• [BioC] readGAlignmentPairs error   Leonard Goldstein
• [BioC] readGappedAlignments and param argument   Elena Grassi
• [BioC] Unusual results with DESeq ?   Osvaldo Graña
• [BioC] Unusual results with DESeq ?   Osvaldo Graña
• [BioC] installation packages   Ivan Gregoretti
• [BioC] rsbml package installation error   Stefan Gries
• [BioC] rsbml package installation error   Stefan Gries
• [BioC] rsbml package installation error   Stefan Gries
• [BioC] plot methylation figure for end analysis   Alex Gutteridge
• [BioC] creating geneset files (.gmt) for GSEA   Nehme Hachem
• [BioC] Gviz - Beginner - Problem reproducing the provided examples   Hahne, Florian
• [BioC] howto plot a figure like UCSC genome browser by Gviz   Hahne, Florian
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Hahne, Florian
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Hahne, Florian
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Hahne, Florian
• [BioC] Horizontal text in Gviz title panel.   Hahne, Florian
• [BioC] affxparser installation error   Kasper Daniel Hansen
• [BioC] bayseq pair data   Tom Hardcastle
• [BioC] Affy HTA 2.0 array analysis   He, Yiwen (NIH/CIT) [C]
• [BioC] unexpected voom! / limma contrast inconsistency   Stephen Hoang
• [BioC] unexpected voom! / limma contrast inconsistency   Stephen Hoang
• [BioC] eayRNASeq with Ensemble GRCh37 help   Aki Hoji
• [BioC] problem with creating array annotation package   Hooiveld, Guido
• [BioC] getBM returns shorter vectors than values   Hans-Rudolf Hotz
• [BioC] confusing P-value of one gene   Wolfgang Huber
• [BioC] confusing P-value of one gene   Wolfgang Huber
• [BioC] longitudinal GWAS analysis   Wolfgang Huber
• [BioC] about coverage profile comparison   Wolfgang Huber
• [BioC] Bioinformatics Position in Oncology / Multiple Myeloma, Univ. Heidelberg   Wolfgang Huber
• [BioC] arrayQualityMetrics: How to observe Hoeffding\'s statistic Da in aqm.maplot object?   Wolfgang Huber
• [BioC] Measuring shifts in intronic expression independently of exons   Wolfgang Huber
• [BioC] BioStrings PairwiseAlignment deletion() insertion() function   Marcin Imielinski
• [BioC] Fwd: BioStrings PairwiseAlignment deletion() insertion() function   Marcin Imielinski
• [BioC] howto plot a figure like UCSC genome browser by Gviz   Robert Ivanek
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Robert Ivanek
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Robert Ivanek
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Robert Ivanek
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Robert Ivanek
• [BioC] PWM with GAPS   Lakshmanan Iyer
• [BioC] Creat PWM from Alignment with Gaps   Lakshmanan Iyer
• [BioC] writeFastq to gzip compressed files   Harris A. Jaffee
• [BioC] (no subject)   Jager, Dominik
• [BioC] Gviz - Beginner - Problem reproducing the provided examples   Jager, Dominik
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Jager, Dominik
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Jager, Dominik
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Jager, Dominik
• [BioC] open position: Bioinformatics Data Analyst @ IMP/Vienna   Jaritz,Markus
• [BioC] Which package I should use   Xiaoben Jiang
• [BioC] Running ComBat in parallel   Johnson, William Evan
• [BioC] Running ComBat in parallel   Johnson, William Evan
• [BioC] sva/ComBat with missing values?   Johnson, William Evan
• [BioC] 8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7   Sarah Jugurnauth-Little
• [BioC] Job offers at Oncology Novartis Basel   Kauffmann, Audrey
• [BioC] Microarray analyses. How to know the direction of the expression?   Mary Kindall
• [BioC] Job: Biostatistician (m/f) - Schwenningen, Germany   Prof. Dr. Matthias Kohl
• [BioC] topGO issues   Pekka Kohonen
• [BioC] how to calculate logFC in limma   Federico Lasa
• [BioC] rsbml package installation error   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] extracting genomic positions of indels from a BAM file   Michael Lawrence
• [BioC] rsbml package installation error   Michael Lawrence
• [BioC] rsbml package installation error   Michael Lawrence
• [BioC] Bioconductor refLocs2TranscriptLocs function   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] readGAlignmentPairs error   Michael Lawrence
• [BioC] Lifting over a bam file with Rsamtools and GenomicRanges   Michael Lawrence
• [BioC] writeFastq to gzip compressed files   Michael Lawrence
• [BioC] writeFastq to gzip compressed files   Michael Lawrence
• [BioC] about autoplot in ggbio   Michael Lawrence
• [BioC] about autoplot in ggbio   Michael Lawrence
• [BioC] about autoplot in ggbio   Michael Lawrence
• [BioC] sva + voom + limma   Jeff Leek
• [BioC] sva: how to incorporate adjusting variables   Jeff Leek
• [BioC] sva/ComBat with missing values?   Jeff Leek
• [BioC] problem to install package CORNA   Martin Leonardo
• [BioC] error in "count" for SummarizedExperiment in easyRNASeq   Francesco Lescai
• [BioC] getBM returns shorter vectors than values   Francesco Lescai
• [BioC] getBM returns shorter vectors than values   Francesco Lescai
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Steve Lianoglou
• [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction   Steve Lianoglou
• [BioC] Microarray analyses. How to know the direction of the expression?   Steve Lianoglou
• [BioC] problem while loading affycoretools   Steve Lianoglou
• [BioC] cycle package question   Steve Lianoglou
• [BioC] cycle package question   Steve Lianoglou
• [BioC] installation packages   Steve Lianoglou
• [BioC] Regarding multiple hits of same read   Steve Lianoglou
• [BioC] installation packages   Steve Lianoglou
• [BioC] Fwd: Regarding multiple hits of same read   Steve Lianoglou
• [BioC] installation packages   Steve Lianoglou
• [BioC] regarding makeTranscriptDbFromGFF   Steve Lianoglou
• [BioC] regarding makeTranscriptDbFromGFF   Steve Lianoglou
• [BioC] GC counts   Steve Lianoglou
• [BioC] package availability for R3.01   E.M. Lodder
• [BioC] package availability for R3.01   E.M. Lodder
• [BioC] package availability for R3.01   E.M. Lodder
• [BioC] package availability for R3.01   E.M. Lodder
• [BioC] accessing NetAffx annotation with "oligo" package   Joao Sollari Lopes
• [BioC] blast probe clusters when using Affymetrix Gene Array Strips   Joao Sollari Lopes
• [BioC] blast probe clusters when using Affymetrix Gene Array Strips   Joao Sollari Lopes
• [BioC] affymtrix transcript_cluster categories   Joao Sollari Lopes
• [BioC] Differential Expressed Genes analysis regarding limited genes   Michael Love
• [BioC] Differential Expressed Genes analysis regarding limited genes   Michael Love
• [BioC] DESeq2 : when the variable of interest is not a factor   Michael Love
• [BioC] DESeq2 : when the variable of interest is not a factor   Michael Love
• [BioC] DESeq2 : when the variable of interest is not a factor   Michael Love
• [BioC] DESeq2 returning NA pvalue when counts are not zero   Michael Love
• [BioC] blast probe clusters when using Affymetrix Gene Array Strips   James W. MacDonald
• [BioC] metabolomics data analysis   James W. MacDonald
• [BioC] metabolomics data analysis   James W. MacDonald
• [BioC] package availability for R3.01   James W. MacDonald
• [BioC] desing matrix and interaction term difficulty   James W. MacDonald
• [BioC] how to convert ExpressionSet to AffyBatch   James W. MacDonald
• [BioC] how to convert ExpressionSet to AffyBatch   James W. MacDonald
• [BioC] Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol   James W. MacDonald
• [BioC] trouble reading DNA stringset from keggGet function   James W. MacDonald
• [BioC] MakeDBPackage fails with SQL error   James W. MacDonald
• [BioC] Differential expression analysis in Limma for one factor after adjusting for a covariate   James W. MacDonald
• [BioC] Agilent two color Quantile normalization   James W. MacDonald
• [BioC] limma - batch dates incorrporated into t-test   James W. MacDonald
• [BioC] limma - batch dates incorrporated into t-test   James W. MacDonald
• [BioC] limma - batch dates incorrporated into t-test   James W. MacDonald
• [BioC] Microarray analyses. How to know the direction of the expression?   James W. MacDonald
• [BioC] Limma normalizeBetweenArrays does not normalize M values using Quantile method directly.???   James W. MacDonald
• [BioC] limma - batch dates incorrporated into t-test   James W. MacDonald
• [BioC] problem while loading affycoretools   James W. MacDonald
• [BioC] problem while loading affycoretools   James W. MacDonald
• [BioC] affymtrix transcript_cluster categories   James W. MacDonald
• [BioC] Importing quantile normalized .txt file to limma for differential expression   James W. MacDonald
• [BioC] Importing quantile normalized .txt file to limma for differential expression   James W. MacDonald
• [BioC] regarding makeTranscriptDbFromGFF   James W. MacDonald
• [BioC] simulating genetic data   James W. MacDonald
• [BioC] org.Hs.eg.db   James W. MacDonald
• [BioC] RSQLite and DB problems   James W. MacDonald
• [BioC] RSQLite and DB problems   James W. MacDonald
• [BioC] GOstats code validation   James W. MacDonald
• [BioC] cycle package question   Alyaa Mahmoud
• [BioC] cycle package question   Alyaa Mahmoud
• [BioC] cycle package question   Alyaa Mahmoud
• [BioC] DESeq2 : when the variable of interest is not a factor   Jose M Garcia Manteiga
• [BioC] DESeq2 : when the variable of interest is not a factor   Jose M Garcia Manteiga
• [BioC] DESeq2 : when the variable of interest is not a factor   Jose M Garcia Manteiga
• [BioC] Useful information about Ensembl release 73 mart databases   Thomas Maurel
• [BioC] Differential expression analysis in Limma for one factor after adjusting for a covariate   Sam McInturf
• [BioC] Unable to load xps   Jorge Melendez
• [BioC] Unable to load xps   Jorge Melendez
• [BioC] Unable to load xps   Jorge Melendez
• [BioC] package availability for R3.01   Martin Morgan
• [BioC] Gviz - Beginner - Problem reproducing the provided examples   Martin Morgan
• [BioC] [devteam-bioc] getGmt error   Martin Morgan
• [BioC] [devteam-bioc] getGmt error   Martin Morgan
• [BioC] bug report in pathview   Martin Morgan
• [BioC] readGappedAlignments and param argument   Martin Morgan
• [BioC] Simple pathway enrichment analysis for gene lists   Martin Morgan
• [BioC] writeFastq to gzip compressed files   Martin Morgan
• [BioC] writeFastq to gzip compressed files   Martin Morgan
• [BioC] Hello   Martin Morgan
• [BioC] Rsamtools: scan all optional tags that exists in my bam file   Martin Morgan
• [BioC] Rsamtools: write a GAlignments object to a bam file   Martin Morgan
• [BioC] Sorting a GAlignments object by QNAME   Martin Morgan
• [BioC] pathview puzzle   Oleg Moskvin
• [BioC] aCGH telling me to run find.hmm.states before merge hmm.states even though I have.   Cian Murphy
• [BioC] SAM for protemics - low q values   Hendrik Nolte
• [BioC] simulating genetic data   Hermann Norpois
• [BioC] Getting Introns Expression at a Per Gene Level   Valerie Obenchain
• [BioC] Getting Introns Expression at a Per Gene Level   Valerie Obenchain
• [BioC] replace nucleotide at fixed position in a DNAStringSet object   Valerie Obenchain
• [BioC] readGAlignmentPairs error   Valerie Obenchain
• [BioC] readGAlignmentPairs error   Valerie Obenchain
• [BioC] [devteam-bioc] GenomicRanges::findOverlap unexpected behaviour with 0 width ranges   Valerie Obenchain
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Valerie Obenchain
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Valerie Obenchain
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Valerie Obenchain
• [BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*   Valerie Obenchain
• [BioC] Imaginary units of complex numbers dropped by 'knitr'   Andrzej Oleś
• [BioC] Imaginary units of complex numbers dropped by 'knitr'   Andrzej Oleś
• [BioC] sva: how to incorporate adjusting variables   Meritxell Oliva
• [BioC] sva + voom + limma   Meritxell Oliva
• [BioC] sva: how to incorporate adjusting variables   Meritxell Oliva
• [BioC] sva + voom + limma. eBayes(trend=TRUE)   Meritxell Oliva
• [BioC] howto plot a figure like UCSC genome browser by Gviz   Ou, Jianhong
• [BioC] howto plot a figure like UCSC genome browser by Gviz   Ou, Jianhong
• [BioC] coverage() in IRanges gives >0 coverage when weight == 0   Ludo Pagie
• [BioC] 'version' is missing error when running makeTxDbPackageFromUCSC   Hervé Pagès
• [BioC] [devteam-bioc] Depth of Coverage and Base counts from BAM file   Hervé Pagès
• [BioC] [devteam-bioc] Depth of Coverage and Base counts from BAM file   Hervé Pagès
• [BioC] BUG: median(IRanges::Rle(NA), na.rm=TRUE)) should return NA   Hervé Pagès
• [BioC] replace nucleotide at fixed position in a DNAStringSet object   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] Biostrings::matchPattern,extract sequences   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] Biostrings::matchPattern,extract sequences   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'   Hervé Pagès
• [BioC] readGAlignmentPairs error   Hervé Pagès
• [BioC] Fwd: BioStrings PairwiseAlignment deletion() insertion() function   Hervé Pagès
• [BioC] Fwd: BioStrings PairwiseAlignment deletion() insertion() function   Hervé Pagès
• [BioC] Sorting a GAlignments object by QNAME   Hervé Pagès
• [BioC] Sorting a GAlignments object by QNAME   Hervé Pagès
• [BioC] Measuring shifts in intronic expression independently of exons   James Perkins
• [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 convert ExpressionSet to AffyBatch   Wang Peter
• [BioC] how to convert ExpressionSet to AffyBatch   Wang Peter
• [BioC] how to calculate logFC in limma   Wang Peter
• [BioC] how to get cel file by getGEO   Wang Peter
• [BioC] how to get cel file by getGEO   Wang Peter
• [BioC] Exception thrown in ReadAffy() when reading Hu-133B files in a GEO Dataset   Peterson, Leif
• [BioC] DESeq2 : when the variable of interest is not a factor   Peterson, Leif
• [BioC] Can't get ComBat in SVA running after SCAN.UPC   Peterson, Leif
• [BioC] Can't get ComBat in SVA running after SCAN.UPC   Peterson, Leif
• [BioC] SCAN.UPC vs NUSE   Leif Peterson
• [BioC] SCAN.UPC vs NUSE   Peterson, Leif
• [BioC] installing bioconductor   Warren Pettitt
• [BioC] SCAN.UPC vs NUSE   Steve Piccolo
• [BioC] Agilent two color Quantile normalization   Neeraj Rana
• [BioC] Agilent two color Quantile normalization   Neeraj Rana
• [BioC] Limma normalizeBetweenArrays does not normalize M values using Quantile method directly.???   Neeraj Rana
• [BioC] preprocessCore load problem in R   Rao,Xiayu
• [BioC] extracting genomic positions of indels from a BAM file   Hubert Rehrauer
• [BioC] Measuring shifts in intronic expression independently of exons   Alejandro Reyes
• [BioC] GSVA questions   Markus Riester
• [BioC] GSVA questions   Markus Riester
• [BioC] Can I input ordinal variables into a model in Limma?   Scott Robinson
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   Scott Robinson
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   Scott Robinson
• [BioC] Running ComBat in parallel   Jeremy Rosenblum
• [BioC] how to get cel file by getGEO   Simona Rossi
• [BioC] GC counts   Devon Ryan
• [BioC] Genes and Metabolites   Avinash S
• [BioC] Regression Analysis   Christian De Santis
• [BioC] Regression Analysis   Christian De Santis
• [BioC] Pathview with non-KEGG organism   Christian De Santis
• [BioC] Pathview - Problem with PNG output   Christian De Santis
• [BioC] Exporting to excell with highlighted changes   Patrick Schorderet
• [BioC] Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions   Paul Shannon
• [BioC] Pathway analysis for differentially expressed genes   Paul Shannon
• [BioC] Simple pathway enrichment analysis for gene lists   Paul Shannon
• [BioC] Simple pathway enrichment analysis for gene lists   Paul Shannon
• [BioC] multiple comparison adjustment of p values in LIMMA   Shi, Tao
• [BioC] multiple comparison adjustment of p values in LIMMA   Shi, Tao
• [BioC] multiple comparison adjustment of p values in LIMMA   Shi, Tao
• [BioC] Rsubread for paired end SOLID sequencing   Wei Shi
• [BioC] Illumina based one color microarray data analysis   Wei Shi
• [BioC] Illumina based one color microarray data analysis   Wei Shi
• [BioC] Hello   Wei Shi
• [BioC] RMA normalization for Affymetrix CEL Files (Subscript out of bounds error)   Sidders, Benjamin
• [BioC] limma - batch dates incorrporated into t-test   Helen Smith
• [BioC] limma - batch dates incorrporated into t-test   Helen Smith
• [BioC] limma - batch dates incorrporated into t-test   Helen Smith
• [BioC] limma - batch dates incorrporated into t-test   Helen Smith
• [BioC] beadarray\'s processSwathData for HumanHT12v4, with 3 swaths   Mike Smith
• [BioC] Can I input ordinal variables into a model in Limma?   Gordon K Smyth
• [BioC] microarray outlier detection   Gordon K Smyth
• [BioC] confusing P-value of one gene   Gordon K Smyth
• [BioC] sva + voom + limma   Gordon K Smyth
• [BioC] multiple comparison adjustment of p values in LIMMA   Gordon K Smyth
• [BioC] multiple comparison adjustment of p values in LIMMA   Gordon K Smyth
• [BioC] unexpected voom! / limma contrast inconsistency   Gordon K Smyth
• [BioC] unexpected voom! / limma contrast inconsistency   Gordon K Smyth
• [BioC] plot methylation figure for end analysis   Michael Stadler
• [BioC] Question about Diffbind input control   Rory Stark
• [BioC] Question about Diffbind input control   Rory Stark
• [BioC] DiffBind for Galaxy   Rory Stark
• [BioC] DiffBind for Galaxy   Rory Stark
• [BioC] PWMEnrich binding site position   Robert Stojnic
• [BioC] problem while loading affycoretools   Mayte Suarez-Farinas
• [BioC] problem while loading affycoretools   Mayte Suarez-Farinas
• [BioC] problem while loading affycoretools   Mayte Suarez-Farinas
• [BioC] problem while loading affycoretools   Mayte Suarez-Farinas
• [BioC] error with dba.counts   Anitha Sundararajan
• [BioC] DiffBind -error with dba.counts   Anitha Sundararajan
• [BioC] DiffBind -error with dba.counts   Anitha Sundararajan
• [BioC] DiffBind -error with dba.counts   Anitha Sundararajan
• [BioC] DiffBind -error with dba.counts   Anitha Sundararajan
• [BioC] DESeq2 : when the variable of interest is not a factor   Marie Sémon
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] about autoplot in ggbio   Bogdan Tanasa
• [BioC] Statistical Bioinformatician Position, Oxford UK   Stephen Taylor
• [BioC] Statistical Bioinformatician Position, Oxford, UK   Stephen Taylor
• [BioC] Error using makeDBPackage() from AnnotationForge package   Gabriel Teku
• [BioC] preprocessCore load problem in R   Dan Tenenbaum
• [BioC] Gviz - Beginner - Problem reproducing the provided examples   Dan Tenenbaum
• [BioC] GSVA questions   Dan Tenenbaum
• [BioC] problem to install package CORNA   Dan Tenenbaum
• [BioC] installing bioconductor   Dan Tenenbaum
• [BioC] Exporting to excell with highlighted changes   Dan Tenenbaum
• [BioC] installation packages   Dan Tenenbaum
• [BioC] problem while loading affycoretools   Dan Tenenbaum
• [BioC] problem while loading affycoretools   Dan Tenenbaum
• [BioC] problem while loading affycoretools   Dan Tenenbaum
• [BioC] DiffBind for Galaxy   Dan Tenenbaum
• [BioC] 'AnnotationDbi' 1.23.24 is required by ‘GO.db’ in Windows   Dan Tenenbaum
• [BioC] Horizontal text in Gviz title panel.   Graham Thomas
• [BioC] unexpected voom! / limma contrast inconsistency   Ryan C. Thompson
• [BioC] plot methylation figure for end analysis   Tim Triche, Jr.
• [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions   Nitesh Turaga
• [BioC] R/S-PLUS Course schedule in US - XLSolutions Corp   Sue Turner
• [BioC] RMA normalization for Affymetrix CEL Files (Subscript out of bounds error)   Gundala Viswanath
• [BioC] Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol   Gundala Viswanath
• [BioC] How to deal with Affymetrix probe that map to multiple genes   Gundala Viswanath
• [BioC] package availability for R3.01   Levi Waldron
• [BioC] Change enzyme code (EC) into gene symbol   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] pathview puzzle   Luo Weijun
• [BioC] bug report in pathview (XML?)   Luo Weijun
• [BioC] Pathway analysis microarray expresssion dataset   Luo Weijun
• [BioC] pathview question   Luo Weijun
• [BioC] Pathview with non-KEGG organism   Luo Weijun
• [BioC] Pathview with non-KEGG organism   Luo Weijun
• [BioC] Pathview - Problem with PNG output   Luo Weijun
• [BioC] Pathview question   Luo Weijun
• [BioC] sva/ComBat with missing values?   Hollis Wright
• [BioC] xps library with mouse gene 1.0 transcript arrays   Assa Yeroslaviz
• [BioC] xps library with mouse gene 1.0 transcript arrays   Assa Yeroslaviz
• [BioC] RSQLite and DB problems   Assa Yeroslaviz
• [BioC] RSQLite and DB problems   Assa Yeroslaviz
• [BioC] about autoplot in ggbio   Tengfei Yin
• [BioC] about autoplot in ggbio   Tengfei Yin
• [BioC] about autoplot in ggbio   Tengfei Yin
• [BioC] about autoplot in ggbio   Tengfei Yin
• [BioC] about autoplot in ggbio   Tengfei Yin
• [BioC] Plots with transparent background in ggbio.   Tengfei Yin
• [BioC] 'AnnotationDbi' 1.23.24 is required by ‘GO.db’ in Windows   Sine Katharina Zambach
• [BioC] Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions   Zhang, Jitao David
• [BioC] Biostrings::matchPattern,extract sequences   Zhu, Lihua (Julie)
• [BioC] help with cleanUpdTSeq for PAS analysis   Zhu, Lihua (Julie)
• [BioC] some question about how to use the ChIPpeakAnno.   Zhu, Lihua (Julie)
• [BioC] Biostrings::matchPattern,extract sequences   Zhu, Lihua (Julie)
• [BioC] Biostrings::matchPattern,extract sequences   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno, getAnnotation question   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno, getAnnotation question   Zhu, Lihua (Julie)
• [BioC] Batch retrieval of transcript and aminoacid lengths for a list of HGNC IDs   Gabriele Zoppoli
• [BioC] problem with TXNAME -> SYMBOL mapping in Homo.sapiens library   Aleksandra Pfeifer [guest]
• [BioC] HTqPCR normalization issues again   Alessandro Guffanti - Elena Brini [guest]
• [BioC] dba.counts error   Anitha Sundararajan [guest]
• [BioC] desing matrix and interaction term difficulty   Brian [guest]
• [BioC] GC counts   Catarina [guest]
• [BioC] Plots with transparent background in ggbio.   Costerwell Khyriem [guest]
• [BioC] GenomicRanges::findOverlap unexpected behaviour with 0 width ranges   Daniel Cameron [guest]
• [BioC] Importing quantile normalized .txt file to limma for differential expression   Dhanjit [guest]
• [BioC] trouble reading DNA stringset from keggGet function   Elliot [guest]
• [BioC] EasyRNAseq - error in building count table - Error in unlist   Felix Frey [guest]
• [BioC] plot methylation figure for end analysis   Gia [guest]
• [BioC] error on microarray expression data   Guest [guest]
• [BioC] GSVA questions   Joe [guest]
• [BioC] GSVA questions   Joe [guest]
• [BioC] getGmt error   Joe [guest]
• [BioC] Unable to load xps   Jorge Melendez [guest]
• [BioC] arrayQualityMetrics: How to observe Hoeffding\'s statistic Da in aqm.maplot object?   Kaj Chokeshaiusaha [guest]
• [BioC] Illumina based one color microarray data analysis   KaushalRaj Chaudhary [guest]
• [BioC] org.Hs.eg.db   Krakno [guest]
• [BioC] Human Transcriptome Array 2.0 chip   Michael Peters [guest]
• [BioC] Finding Candidate Binding Sites for multiple Known Transcription Factors simultaneously   Nazia Ahmad [guest]
• [BioC] ChIPpeakAnno, getAnnotation question   Neha [guest]
• [BioC] Computing large correlations in R   Paul [guest]
• [BioC] ddCt calculation and statistics   Peruzza Luca [guest]
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   Scott Robinson [guest]
• [BioC] Error: package \'mzR\' could not be loaded   Siebolt de Boer [guest]
• [BioC] DESeq2 returning NA pvalue when counts are not zero   Ying Ying Sung [guest]
• [BioC] MEDIPS saturation error   Yuting Liu [guest]
• [BioC] bayseq pair data   alice [guest]
• [BioC] metabolomics data analysis   guest [guest]
• [BioC] Pathway analysis for differentially expressed genes   kaushal Raj Chaudhary [guest]
• [BioC] Pathway analysis microarray expresssion dataset   kaushal Raj Chaudhary [guest]
• [BioC] topGO issues   kaushal Raj Chaudhary [guest]
• [BioC] GOstats code validation   kaushal Raj Chaudhary [guest]
• [BioC] PWMEnrich binding site position   massimo acquaviva [guest]
• [BioC] design issue arrays   michela riba [guest]
• [BioC] design issue arrays   michela riba [guest]
• [BioC] Lifting over a bam file with Rsamtools and GenomicRanges   rubi [guest]
• [BioC] Rsamtools: scan all optional tags that exists in my bam file   rubi [guest]
• [BioC] Rsamtools: write a GAlignments object to a bam file   rubi [guest]
• [BioC] Sorting a GAlignments object by QNAME   rubi [guest]
• [BioC] bug report in pathview   shang [guest]
• [BioC] QC for HT HGU133A and U133A X3P   b a
• [BioC] QC for HT HGU133A and U133A X3P   b a
• [BioC] affxparser installation error   ying chen
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   cstrato
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   cstrato
• [BioC] How does one deal with spatial effects detected on single channel microarrays?   cstrato
• [BioC] Unable to load xps   cstrato
• [BioC] Unable to load xps   cstrato
• [BioC] Unable to load xps   cstrato
• [BioC] Unable to load xps   cstrato
• [BioC] Unable to load xps   cstrato
• [BioC] problem with creating array annotation package   cstrato
• [BioC] RLE plot from expression dataset   cstrato
• [BioC] xps library with mouse gene 1.0 transcript arrays   cstrato
• [BioC] xps library with mouse gene 1.0 transcript arrays   cstrato
• [BioC] Regarding multiple hits of same read   deepika lakhwani
• [BioC] Fwd: Regarding multiple hits of same read   deepika lakhwani
• [BioC] Fwd: Regarding multiple hits of same read   deepika lakhwani
• [BioC] regarding makeTranscriptDbFromGFF   deepika lakhwani
• [BioC] regarding makeTranscriptDbFromGFF   deepika lakhwani
• [BioC] regarding makeTranscriptDbFromGFF   deepika lakhwani
• [BioC] plot methylation figure for end analysis   bach le
• [BioC] Genes and Metabolites   n omranian
• [BioC] genes and metabolite   n omranian
• [BioC] about coverage profile comparison   rcaloger
• [BioC] Sorting a GAlignments object by QNAME   nimrod rubinstein
• [BioC] Hello   jayakumar sivalingam
• [BioC] Hello   jayakumar sivalingam
• [BioC] installation packages   fran vino
• [BioC] installation packages   fran vino
• [BioC] installation packages   fran vino
• [BioC] installation packages   fran vino
• [BioC] Bioconductor/R workshop for high-throughput data analysis (web version)   gregory voisin
• [BioC] Differential Expressed Genes analysis regarding limited genes   邵建明

Last message date: Mon Sep 30 21:40:54 CEST 2013
Archived on: Mon Sep 30 23:40:17 CEST 2013

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