July 2013 Archives by thread

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Starting: Mon Jul 1 03:07:03 CEST 2013
Ending: Wed Jul 31 22:59:13 CEST 2013
Messages: 579

• [BioC] using a gtf file to map reads   Valerie Obenchain
  • [BioC] using a gtf file to map reads   Alejandro Reyes
    • [BioC] using a gtf file to map reads   Michael Love
• [BioC] BioC 2013, July 17 (Developer Day) 18-19: 'Early' registration deadline July 1   Martin Morgan
• [BioC] [bioc] correlation analysis of RNA-seq   Makis Motakis
  • [BioC] [bioc] correlation analysis of RNA-seq   Wolfgang Huber
  • [BioC] [bioc] correlation analysis of RNA-seq   Gordon K Smyth
• [BioC] sample probe profile or sample gene profile   Francisco Ortuno [guest]
• [BioC] edgeR dispersion value   Tiago Jesus [guest]
  • [BioC] edgeR dispersion value   Mark Robinson
• [BioC] PCA-3D Plot   Chevala V V S Narayana [guest]
  • [BioC] PCA-3D Plot   James W. MacDonald
    • [BioC] PCA-3D Plot   Veera Venkata Satyanarayana
      • [BioC] PCA-3D Plot   James W. MacDonald
      • [BioC] PCA-3D Plot   Veera Venkata Satyanarayana
      • [BioC] PCA-3D Plot   Steve Lianoglou
      • [BioC] PCA-3D Plot   Veera Venkata Satyanarayana
      • [BioC] PCA-3D Plot   Veera Venkata Satyanarayana
      • [BioC] PCA-3D Plot   James W. MacDonald
• [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
  • [BioC] Repeated Measures mRNA expression analysis   James W. MacDonald
    • [BioC] Repeated Measures mRNA expression analysis   Gordon K Smyth
      • [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
      • [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
      • [BioC] Repeated Measures mRNA expression analysis   Gordon K Smyth
      • [BioC] Repeated Measures mRNA expression analysis   Gordon K Smyth
• [BioC] rtracklayer   Johannes Waage
  • [BioC] rtracklayer   James W. MacDonald
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   James W. MacDonald
  • [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Victoria Svinti
• [BioC] info on pathview   Luo Weijun
• [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
  • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   James W. MacDonald
    • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Ed Schwalbe
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
    • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
  • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Tim Triche, Jr.
    • [BioC] featureCounts read summarization function   Wei Shi
      • [BioC] featureCounts read summarization function   Diego Diez
      • [BioC] featureCounts read summarization function   Wei Shi
      • [BioC] featureCounts read summarization function   Diego Diez
      • [BioC] featureCounts read summarization function   Tim Triche, Jr.
      • [BioC] featureCounts read summarization function   Tim Triche, Jr.
      • [BioC] featureCounts read summarization function   Wei Shi
      • [BioC] featureCounts read summarization function   Diego Diez
      • [BioC] featureCounts read summarization function   Wei Shi
    • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Tim Triche, Jr.
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Tim Triche, Jr.
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Simone
      • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Tim Triche, Jr.
  • [BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?   Victoria Svinti
• [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   William D'Avigdor
  • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   Wei Shi
    • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   Wei Shi
      • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   Wil D'Avigdor
      • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   Wei Shi
      • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   William D'Avigdor
      • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   Wei Shi
      • [BioC] Illumina Probe_ID used in the LIMMA package for neqc function   William D'Avigdor
• [BioC] Different colors in vennDiagram?   Leif Väremo
  • [BioC] Different colors in vennDiagram?   Dan Du
• [BioC] Study design in DEXSeq   Antonio Domingues
  • [BioC] Study design in DEXSeq   Alejandro Reyes
    • [BioC] Study design in DEXSeq   Antonio Domingues
• [BioC] read.ilmn() and variation between chips   Rao,Xiayu
  • [BioC] read.ilmn() and variation between chips   Wei Shi
    • [BioC] read.ilmn() and variation between chips   Rao,Xiayu
  • [BioC] read.ilmn() and variation between chips   Gordon K Smyth
    • [BioC] read.ilmn() and variation between chips   Rao,Xiayu
• [BioC] limma: tissue specific genes using voom   Jaaved Mohammed
• [BioC] DEXSeq questions on power and counting bins   Gu [guest]
  • [BioC] DEXSeq questions on power and counting bins   Wolfgang Huber
• [BioC] technical + biological replicate design for multiple categories   James Platt
  • [BioC] technical + biological replicate design for multiple categories   Naomi Altman
  • [BioC] technical + biological replicate design for multiple categories   James Platt
    • [BioC] technical + biological replicate design for multiple categories   Naomi Altman
• [BioC] How to create a heatmap of a gene family (using subset of exprs(vsd) in DESeq)   Theresa Hodges [guest]
  • [BioC] How to create a heatmap of a gene family (using subset of exprs(vsd) in DESeq)   Wolfgang Huber
• [BioC] Question about mget vs. select for annotation package   Christina Chaivorapol
  • [BioC] Question about mget vs. select for annotation package   Hervé Pagès
    • [BioC] Question about mget vs. select for annotation package   Marc Carlson
• [BioC] merging two data frames   chris Jhon
• [BioC] Merging two data frame   chris Jhon
  • [BioC] Merging two data frame   Alyaa Mahmoud
    • [BioC] Merging two data frame   chris Jhon
  • [BioC] Merging two data frame   Steve Lianoglou
• [BioC] Normalize background on marray Agilent object   Guillermo Marco Puche
  • [BioC] Normalize background on marray Agilent object   Gordon K Smyth
    • [BioC] Normalize background on marray Agilent object   Guillermo Marco Puche
  • [BioC] Normalize background on marray Agilent object   Gordon K Smyth
• [BioC] getting genotypes with oligo package   Lilia Romdhane [guest]
• [BioC] Flow Cytometry Analysis with FlowCore   Telma Fernandes [guest]
  • [BioC] Flow Cytometry Analysis with FlowCore   Mike
  • [BioC] Flow Cytometry Analysis with FlowCore   Jiang, Mike
• [BioC] Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values   Pilling, Luke
  • [BioC] Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values   Kasper Daniel Hansen
    • [BioC] Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values   Pilling, Luke
• [BioC] romer implementation in edgeR   Pekka Kohonen
  • [BioC] romer implementation in edgeR   Gordon K Smyth
    • [BioC] romer implementation in edgeR   julie.leonard at syngenta.com
• [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Robert Castelo
  • [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Paul Shannon
    • [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Robert Castelo
      • [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Paul Shannon
      • [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Robert Castelo
      • [BioC] graph::edgeMatrix() fails for signature(object="graphBAM")   Paul Shannon
• [BioC] edgeR uneven group sizes   Charles Determan Jr
  • [BioC] edgeR uneven group sizes   Gordon K Smyth
    • [BioC] edgeR uneven group sizes   Charles Determan Jr
      • [BioC] edgeR uneven group sizes   Gordon K Smyth
      • [BioC] edgeR uneven group sizes   Charles Determan Jr
• [BioC] What is the FDR set to for the BH method.   Cornish, Joseph (NIH/NIAID) [F]
  • [BioC] What is the FDR set to for the BH method.   Naomi Altman
• [BioC] RJpGene.1.0 and RCnGene.1.0 .CDF files   Ayelen [guest]
  • [BioC] RJpGene.1.0 and RCnGene.1.0 .CDF files   James W. MacDonald
• [BioC] GWATools use in creating ncdf files   Sam Rose
  • [BioC] GWATools use in creating ncdf files   Stephanie M. Gogarten
• [BioC] Use which method to calculate q-value or adjusted p-value   Feng Tian
  • [BioC] Use which method to calculate q-value or adjusted p-value   Tim Triche, Jr.
    • [BioC] Use which method to calculate q-value or adjusted p-value   Feng Tian
      • [BioC] Use which method to calculate q-value or adjusted p-value   Tim Triche, Jr.
• [BioC] Start and End positions in the GTF/GFF3 files   Delasa Aghamirzaie
  • [BioC] Start and End positions in the GTF/GFF3 files   Hervé Pagès
• [BioC] Coercing SimpleList to CompressedList objects   Leonard Goldstein
  • [BioC] Coercing SimpleList to CompressedList objects   Martin Morgan
    • [BioC] Coercing SimpleList to CompressedList objects   Michael Lawrence
• [BioC] summarizeOverlaps with mapq filter?   Sang Chul Choi
  • [BioC] summarizeOverlaps with mapq filter?   Valerie Obenchain
• [BioC] org.Hs.eg.db namespace issue   Anthony Bosco
  • [BioC] org.Hs.eg.db namespace issue   Dan Tenenbaum
  • [BioC] org.Hs.eg.db namespace issue   Dan Tenenbaum
    • [BioC] org.Hs.eg.db namespace issue   Anthony Bosco
• [BioC] Identifying expression trends in RNA-seq experiment - through edgeR   Sandhya Pemmasani Kiran
• [BioC] Comparing log FC edgeR   Alpesh Querer
  • [BioC] Comparing log FC edgeR   Gordon K Smyth
• [BioC] Problem running pathview due to broken XML package   Luo Weijun
• [BioC] Blast a BSgenome   Ugo Borello
  • [BioC] Blast a BSgenome   Hervé Pagès
    • [BioC] Blast a BSgenome   Ugo Borello
• [BioC] Venn diagrams using ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] nsFilter error in genefilter   steven wink
  • [BioC] nsFilter error in genefilter   James W. MacDonald
• [BioC] DEXSeq Help Needed: newExonCountSet() error messages   Margaret Linan
  • [BioC] DEXSeq Help Needed: newExonCountSet() error messages   Wolfgang Huber
• [BioC] Excluding probes during methylation analysis   Victoria Svinti
  • [BioC] Excluding probes during methylation analysis   Tim Triche, Jr.
    • [BioC] Excluding probes during methylation analysis   Victoria Svinti
      • [BioC] Excluding probes during methylation analysis   Tim Triche, Jr.
      • [BioC] Excluding probes during methylation analysis   Victoria Svinti
• [BioC] ReadGappedAlignments and FindOverlaps   Eric Foss [guest]
  • [BioC] ReadGappedAlignments and FindOverlaps   Michael Lawrence
• [BioC] xps- not being able to load   Juehua Yu
  • [BioC] xps- not being able to load   cstrato
    • [BioC] xps- not being able to load   Juehua Yu
      • [BioC] xps- not being able to load   cstrato
• [BioC] bsseq in devel   Kasper Daniel Hansen
  • [BioC] bsseq in devel   Tim Triche, Jr.
• [BioC] Failed to obtain \'hguid\' cookie for UCSC browser session   Ania [guest]
  • [BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session   Dan Tenenbaum
    • [BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session   Michael Lawrence
    • [BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session   Anna Sawicka
      • [BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session   Erik van den Akker
      • [BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session   Martin Morgan
• [BioC] Error in clusterProfiler package with function \"setReadable<-\"   Frederic Bertrand [guest]
  • [BioC] Error in clusterProfiler package with function \"setReadable<-\"   Dan Tenenbaum
    • [BioC] Error in clusterProfiler package with function \"setReadable<-\"   Dan Tenenbaum
      • [BioC] Error in clusterProfiler package with function \"setReadable<-\"   Frédéric Bertrand
  • [BioC] Error in clusterProfiler package with function \"setReadable<-\"   Martin Morgan
• [BioC] how to do a paired analysis with minfi?   Pablo marin-garcia
  • [BioC] how to do a paired analysis with minfi?   Kasper Daniel Hansen
• [BioC] Open position for a Core Bioinformatician in Lund, Sweden   _Bio - Informatics
• [BioC] Can we apply WGCNA to RNA-seq dataset?   faranak
• [BioC] Gviz import bed file for AnnotationTrack   Hahne, Florian
• [BioC] SeqGSEA estiGeneNBstat()   Kasoji, Manjula (NIH/NCI) [C]
  • [BioC] SeqGSEA estiGeneNBstat()   Xi Wang
• [BioC] an error in is CDFXDA   James W. MacDonald
• [BioC] human miRNA predicted/validated targets   Ranjani R [guest]
  • [BioC] human miRNA predicted/validated targets   James W. MacDonald
    • [BioC] comBat or PCA to adjust for hidden variables in a high-throughput qPCR experiment with only 120 genes measured   shirley zhang
• [BioC] illumina microarray and affymetrix exon array data   Rao,Xiayu
• [BioC] getSYMBOL( ) error   Rao,Xiayu
  • [BioC] getSYMBOL( ) error   James W. MacDonald
    • [BioC] getSYMBOL( ) error   Rao,Xiayu
• [BioC] test qPCR data for differential expression   Andreia Fonseca
• [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   zhengyu jiang
  • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Peter Langfelder
    • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Peter Langfelder
  • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Gordon K Smyth
    • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Gordon K Smyth
      • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Gordon K Smyth
    • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   zhengyu jiang
      • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Gordon K Smyth
      • [BioC] limma for homemade microarray - question on NAs and multiple probes for one gene   Wang Peter
• [BioC] BioC2013 Afternoon Lab schedule now online   Dan Tenenbaum
• [BioC] pd.hugene.2.0.st missing normgene->exon mappings   Mark Cowley
  • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   James W. MacDonald
    • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   cstrato
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   James W. MacDonald
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   cstrato
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   James W. MacDonald
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   cstrato
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   Mark Cowley
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   James W. MacDonald
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   James W. MacDonald
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   cstrato
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   Mark Cowley
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   cstrato
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   Benilton Carvalho
      • [BioC] pd.hugene.2.0.st missing normgene->exon mappings   Mark Cowley
• [BioC] Bioconductor on Cygwin: mingw/math.h not found   Enrico Ferrero [guest]
• [BioC] Updated affy package? ReadAffy/ AffyBatch has change and breaks my pipeline!   elliott harrison
• [BioC] DESeq2 test over all timepoints?   Charles Determan Jr
  • [BioC] DESeq2 test over all timepoints?   Michael Love
• [BioC] MetaboLights, wiff-files   Forst, Christian
• [BioC] BioC2013: only 9 more slots left!   Dan Tenenbaum
• [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
  • [BioC] Filtering BAM files by start position for VariantTools   Valerie Obenchain
    • [BioC] Filtering BAM files by start position for VariantTools   Valerie Obenchain
    • [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
      • [BioC] Filtering BAM files by start position for VariantTools   Valerie Obenchain
      • [BioC] Filtering BAM files by start position for VariantTools   Valerie Obenchain
      • [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
      • [BioC] Filtering BAM files by start position for VariantTools   Hervé Pagès
      • [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
      • [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
      • [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
      • [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
      • [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
      • [BioC] Filtering BAM files by start position for VariantTools   Michael Lawrence
      • [BioC] Filtering BAM files by start position for VariantTools   Hervé Pagès
      • [BioC] Filtering BAM files by start position for VariantTools   Taylor, Sean D
• [BioC] limma: one sample t-test + covariate   Hooiveld, Guido
  • [BioC] limma: one sample t-test + covariate   Hooiveld, Guido
    • [BioC] limma: one sample t-test + covariate   James W. MacDonald
• [BioC] Best PTC compnay in USA and world   Mkho [guest]
• [BioC] about org.Hs.eg.db package install on linux   sk [guest]
  • [BioC] about org.Hs.eg.db package install on linux   Dan Tenenbaum
• [BioC] additional info on limma models and contrasts   Susan Huse
  • [BioC] additional info on limma models and contrasts   James W. MacDonald
• [BioC] Query regarding "pathview"   Luo Weijun
• [BioC] SeqGSEA skip DS portion   SeqGSEA user [guest]
  • [BioC] SeqGSEA skip DS portion   SeqGSEA user [guest]
    • [BioC] SeqGSEA skip DS portion   Xi Wang
• [BioC] MakeDBPackage fails with SQL error   Scott Presnell [guest]
  • [BioC] MakeDBPackage fails with SQL error   Scott Presnell
• [BioC] about GenomicRanges keepseqlevel deprecation and ggbio   Pablo marin-garcia
  • [BioC] about GenomicRanges keepseqlevel deprecation and ggbio   Michael Lawrence
    • [BioC] about GenomicRanges keepseqlevel deprecation and ggbio   Pablo marin-garcia
      • [BioC] about GenomicRanges keepseqlevel deprecation and ggbio   Tengfei Yin
      • [BioC] about GenomicRanges keepseqlevel deprecation and ggbio   Pablo marin-garcia
• [BioC] package \"affyPLM\" install errors on linux   sk [guest]
  • [BioC] package \"affyPLM\" install errors on linux   Vincent Carey
• [BioC] sum of columns   chris Jhon
  • [BioC] sum of columns   chris Jhon
    • [BioC] sum of columns   chris Jhon
      • [BioC] sum of columns   chris Jhon
      • [BioC] sum of columns   Steve Lianoglou
• [BioC] limma: correcting for a correlation between contrasts   Alex Gutteridge
  • [BioC] limma: correcting for a correlation between contrasts   Gordon K Smyth
    • [BioC] limma: correcting for a correlation between contrasts   Alex Gutteridge
      • [BioC] limma: correcting for a correlation between contrasts   Gordon K Smyth
      • [BioC] limma: correcting for a correlation between contrasts   Gordon K Smyth
• [BioC] simple   Scott Robinson [guest]
  • [BioC] simple   James W. MacDonald
    • [BioC] simple   Kasper Daniel Hansen
      • [BioC] simple   Scott Robinson
• [BioC] mock comparison p-value histogram in DEXSeq   Gu [guest]
  • [BioC] mock comparison p-value histogram in DEXSeq   Alejandro Reyes
    • [BioC] voom   Ina Hoeschele
      • [BioC] voom   Wolfgang Huber
      • [BioC] voom   Ina Hoeschele
• [BioC] DEXSeq - multiple conditions   Manoj Hariharan
  • [BioC] DEXSeq - multiple conditions   Steve Lianoglou
    • [BioC] DEXSeq - multiple conditions   Manoj Hariharan
• [BioC] Job: Scientific Programmer at Breakthrough Breast Cancer, KCL, Guy's Hospital Campus   Lawler, Katherine
• [BioC] readPositionalInfo in snapCGH for preparing CNA files for DNAcopy   Bernard North [guest]
• [BioC] IRanges is broken in Cygwin (mingw/math.h)   Enrico Ferrero
  • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Michael Lawrence
    • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Enrico Ferrero
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Michael Lawrence
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Enrico Ferrero
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Steve Lianoglou
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Enrico Ferrero
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Michael Lawrence
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Martin Morgan
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Enrico Ferrero
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Martin Morgan
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   marco atzeri
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Kasper Daniel Hansen
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Michael Lawrence
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Siefker, Ed B.
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   marco atzeri
      • [BioC] IRanges is broken in Cygwin (mingw/math.h)   Michael Lawrence
• [BioC] Pathview: all NA's in the mapped gene data   Luo Weijun
• [BioC] Correcting for batch effect between two batches of interleaved timepoints   Ryan C. Thompson
• [BioC] Matrix, grid and margin   Servant Nicolas
  • [BioC] Matrix, grid and margin   James W. MacDonald
• [BioC] Problem installing \'survival\' package/ Fix request + other options?   Ranjani R [guest]
  • [BioC] Problem installing \'survival\' package/ Fix request + other options?   Dan Tenenbaum
  • [BioC] Problem installing \'survival\' package/ Fix request + other options?   James W. MacDonald
• [BioC] Import a text file   Chirag Gupta
  • [BioC] Import a text file   Sylvain Brohée
    • [BioC] Import a text file   Chirag Gupta
• [BioC] Using gcrma with \"Affymetrix GeneChip miRNA v1.0\" data   Scott Robinson [guest]
  • [BioC] Using gcrma with \"Affymetrix GeneChip miRNA v1.0\" data   Sean Davis
• [BioC] GEOquery: incomplete feature data from GPL soft file   Sean Davis
• [BioC] cummeRbund   Belmont, John W
• [BioC] About Quality Control using affyPLM package   chittabrata mal
  • [BioC] About Quality Control using affyPLM package   chittabrata mal
• [BioC] Error: cannot allocate vector of size   chittabrata mal
  • [BioC] Error: cannot allocate vector of size   James W. MacDonald
    • [BioC] Error: cannot allocate vector of size   Steve Lianoglou
      • [BioC] Error: cannot allocate vector of size   Martin Morgan
• [BioC] HTqPCR problem with creation of qPCRset   Brian Caffrey
• [BioC] AWS cluster not finding installed R packages   John [guest]
  • [BioC] AWS cluster not finding installed R packages   Dan Tenenbaum
    • [BioC] AWS cluster not finding installed R packages   John K DeHart
  • [BioC] AWS cluster not finding installed R packages   john at enginetix.com
  • [BioC] AWS cluster not finding installed R packages   Dan Tenenbaum
  • [BioC] AWS cluster not finding installed R packages   Dan Tenenbaum
• [BioC] 3 empty plots when I use qvalue   Emma Timmins-Schiffman
• [BioC] DESeq. Error message on estimateDispersions blind   Alex Koeppel
  • [BioC] DESeq. Error message on estimateDispersions blind   Simon Anders
    • [BioC] DESeq. Error message on estimateDispersions blind   Alex Koeppel
• [BioC] Converting PDict to DNAStringSet?   Ryan C. Thompson
• [BioC] DESeq2 design formula error?   Charles Determan Jr
  • [BioC] DESeq2 design formula error?   Steve Lianoglou
    • [BioC] DESeq2 design formula error?   Charles Determan Jr
      • [BioC] DESeq2 design formula error?   Steve Lianoglou
      • [BioC] DESeq2 design formula error?   Jose Garcia
• [BioC] RNAseq machine learning classifier   Michael Breen
  • [BioC] RNAseq machine learning classifier   Steve Lianoglou
    • [BioC] RNAseq machine learning classifier   Michael Breen
  • [BioC] RNAseq machine learning classifier   jhua at tgen.org
    • [BioC] RNAseq machine learning classifier   Wolfgang Huber
      • [BioC] RNAseq machine learning classifier   jhua at tgen.org
      • [BioC] RNAseq machine learning classifier   Michael Love
      • [BioC] RNAseq machine learning classifier   jhua at tgen.org
      • [BioC] RNAseq machine learning classifier   Michael Love
      • [BioC] RNAseq machine learning classifier   Simon Anders
      • [BioC] RNAseq machine learning classifier   jhua at tgen.org
      • [BioC] RNAseq machine learning classifier   Michael Love
      • [BioC] RNAseq machine learning classifier   jhua at tgen.org
    • [BioC] use Combat to adjust for hidden variables without knowing batch effect   shirley zhang
      • [BioC] use Combat to adjust for hidden variables without knowing batch effect   Michael Breen
      • [BioC] use Combat to adjust for hidden variables without knowing batch effect   shirley zhang
      • [BioC] use Combat to adjust for hidden variables without knowing batch effect   Johnson, William Evan
      • [BioC] use Combat to adjust for hidden variables without knowing batch effect   Johnson, William Evan
      • [BioC] use Combat to adjust for hidden variables without knowing batch effect   shirley zhang
• [BioC] filterBam   rcaloger
  • [BioC] filterBam   Martin Morgan
  • [BioC] filterBam   rcaloger
    • [BioC] filterBam   Martin Morgan
    • [BioC] filterBam   rcaloger
      • [BioC] filterBam   Martin Morgan
• [BioC] input format for Mfuzz clustering   Fix Ace
  • [BioC] cselection matrix results   Fix Ace
    • [BioC] forgot to mention this function is from Mfuzz package--Re: cselection matrix results   Fix Ace
      • [BioC] HT-Seq count and GTF   Jose M Garcia Manteiga
      • [BioC] HT-Seq count and GTF   Jose M Garcia Manteiga
      • [BioC] HT-Seq count and GTF   Steve Lianoglou
      • [BioC] HT-Seq count and GTF   Simon Anders
• [BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   Martin Rijlaarsdam
  • [BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   Martin Rijlaarsdam
    • [BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   Robert Ivanek
• [BioC] Contingency tests in R, Error with large numbers   Gibbons, John G
• [BioC] symbol and filtering -affy hugene ST 1.0 -oligo limma   Rao,Xiayu
• [BioC] getting a list of genomic sequences from a list of gene names   Paul Shannon
  • [BioC] getting a list of genomic sequences from a list of gene names   Michael Lawrence
    • [BioC] getting a list of genomic sequences from a list of gene names   Paul Shannon
      • [BioC] getting a list of genomic sequences from a list of gene names   Hervé Pagès
      • [BioC] getting a list of genomic sequences from a list of gene names   Paul Shannon
    • [BioC] getting a list of genomic sequences from a list of gene names   Hervé Pagès
• [BioC] GRange - append metadata from a dataframe   Hermann Norpois
  • [BioC] GRange - append metadata from a dataframe   Michael Lawrence
• [BioC] job advertisement   Zhenyu Xu
• [BioC] Rgraphviz multiline edge label   Ludovica Montanucci [guest]
  • [BioC] Rgraphviz multiline edge label   Vincent Carey
• [BioC] Bsgenome gap mask conundrum   Ugo Borello
• [BioC] TranscriptDb object to RangedData for ChIPpeakAnno   Alan Smith
  • [BioC] TranscriptDb object to RangedData for ChIPpeakAnno   Alan Smith
  • [BioC] TranscriptDb object to RangedData for ChIPpeakAnno   Ou, Jianhong
    • [BioC] TranscriptDb object to RangedData for ChIPpeakAnno   Alan Smith
• [BioC] Doubt on time course design   Stefano Capomaccio [guest]
  • [BioC] Doubt on time course design   Aliaksei Holik
    • [BioC] Doubt on time course design   Aliaksei Holik
      • [BioC] Doubt on time course design   Stefano Capomaccio
• [BioC] Vector for Targest in Tquantile Normalization for different groups.   neeraj rana
  • [BioC] Limma Multi-level Experiments   Michael Breen
    • [BioC] Limma Multi-level Experiments   P.D. Moerland
    • [BioC] Limma Multi-level Experiments   Michael Breen
• [BioC] cyber-T error   Matthew McCormack
• [BioC] Question about quality of biological replicates when using edgeR   pbczyd .
• [BioC] Way to extract population specific genotype from 1000 genome   Prashantha Hebbar
  • [BioC] Way to extract population specific genotype from 1000 genome   Vincent Carey
• [BioC] about the package edgeR   Georgia Petridou
• [BioC] Vector for Targest in Tquantile Normalization for different groups   Gordon K Smyth
• [BioC] GeneticsPed Pedigree object creation error: recursive indexing failed at level 2   Liz Hare
  • [BioC] GeneticsPed Pedigree object creation error: recursive indexing failed at level 2   Dan Tenenbaum
    • [BioC] GeneticsPed Pedigree object creation error: recursive indexing failed at level 2   David Henderson
• [BioC] HTqPCR problems   Diane Guevremont
• [BioC] read.HTSeqCounts with count matrix   Alpesh Querer
• [BioC] Too many (?) differentially expressed genes - edgeR and DESeq   Darya Vanichkina
  • [BioC] Too many (?) differentially expressed genes - edgeR and DESeq   Wolfgang Huber
    • [BioC] Too many (?) differentially expressed genes - edgeR and DESeq   Darya Vanichkina
      • [BioC] Too many (?) differentially expressed genes - edgeR and DESeq   Simon Anders
• [BioC] Prolems with AraGene 1_1 annotation   Hugh Shanahan
  • [BioC] Prolems with AraGene 1_1 annotation   James W. MacDonald
• [BioC] edgeR - filtering criteria   Catarina Almeida
  • [BioC] edgeR - filtering criteria   Steve Lianoglou
• [BioC] Question about quality of biological replicates from RNAseq data   pbczyd .
• [BioC] Trimming of partial adaptor sequences   Taylor, Sean D
  • [BioC] Trimming of partial adaptor sequences   Devon Ryan
  • [BioC] Trimming of partial adaptor sequences   James W. MacDonald
  • [BioC] Trimming of partial adaptor sequences   Ryan C. Thompson
  • [BioC] Trimming of partial adaptor sequences   Stijn van Dongen
  • [BioC] Trimming of partial adaptor sequences   Hervé Pagès
    • [BioC] Trimming of partial adaptor sequences   Michael Stadler
    • [BioC] Trimming of partial adaptor sequences   Taylor, Sean D
      • [BioC] Trimming of partial adaptor sequences   Harris A. Jaffee
      • [BioC] Trimming of partial adaptor sequences   Taylor, Sean D
      • [BioC] Trimming of partial adaptor sequences   Harris A. Jaffee
      • [BioC] Trimming of partial adaptor sequences   Hervé Pagès
      • [BioC] Trimming of partial adaptor sequences   Hervé Pagès
      • [BioC] Trimming of partial adaptor sequences   Harris A. Jaffee
    • [BioC] Trimming of partial adaptor sequences   Taylor, Sean D
• [BioC] ERROR: compilation failed for package XVector   Pengcheng Yang
  • [BioC] ERROR: compilation failed for package XVector   Hervé Pagès
    • [BioC] ERROR: compilation failed for package XVector   Pengcheng Yang
      • [BioC] ERROR: compilation failed for package XVector   Dan Tenenbaum
      • [BioC] ERROR: compilation failed for package XVector   Hervé Pagès
      • [BioC] ERROR: compilation failed for package XVector   Pengcheng Yang
      • [BioC] ERROR: compilation failed for package XVector   Pengcheng Yang
• [BioC] Job reminder: Open position for a Core Bioinformatician in Lund, Sweden   _Bio - Informatics
• [BioC] Paired RankProducts analysis   Jon Manning
• [BioC] Conservative results using DEXSeq   Gu [guest]
  • [BioC] Conservative results using DEXSeq   Simon Anders
    • [BioC] Fwd: Conservative results using DEXSeq   Levi Waldron
      • [BioC] Conservative results using DEXSeq   Wolfgang Huber
• [BioC] How to transform a fastq object in granges?   Frederic Fournier
  • [BioC] How to transform a fastq object in granges?   Valerie Obenchain
• [BioC] Using DESeq normalized gene count to replace FPKM?   Jike Cui
  • [BioC] Using DESeq normalized gene count to replace FPKM?   Simon Anders
• [BioC] DiffBind & Chip-exo   Rory Stark
  • [BioC] DiffBind & Chip-exo   Rory Stark
• [BioC] Access source code of internal function within R   heyi xiao
  • [BioC] Access source code of internal function within R   Dan Tenenbaum
• [BioC] Problem with decideTests - No p-val correction   Atul Kakrana
  • [BioC] Problem with decideTests - No p-val correction   James W. MacDonald
    • [BioC] Problem with decideTests - No p-val correction   Atul Kakrana
• [BioC] Problem using getGEO   Nick Goelz
  • [BioC] Problem using getGEO   Dan Tenenbaum
    • [BioC] Problem using getGEO   Dan Tenenbaum
• [BioC] Suggestion - gene set enrichment of genes against BP and Disease gene sets   Atul Kakrana
• [BioC] Pathview published in Bioinformatics   km
• [BioC] Limma Design for Paired Samples Question   Fazelzadeh, Parastoo
• [BioC] Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)   Luo Weijun
• [BioC] GSE states   Lina Thomas [guest]
  • [BioC] GSE states   Tim Triche, Jr.
    • [BioC] GSE states   Tim Triche, Jr.
      • [BioC] GSE states   Tim Triche, Jr.
      • [BioC] GSE states   Lina Thomas
      • [BioC] GSE states   Tim Triche, Jr.
      • [BioC] GSE states   Levi Waldron
      • [BioC] GSE states   Tim Triche, Jr.
      • [BioC] GSE states   Lina Thomas
• [BioC] Error in locateVariants   Jolly Shrivastava
  • [BioC] Error in locateVariants   Valerie Obenchain
    • [BioC] Error in locateVariants   Valerie Obenchain
• [BioC] Remove samples and probes from Illumina 450K data   Donglei Hu [guest]
  • [BioC] Remove samples and probes from Illumina 450K data   James W. MacDonald
• [BioC] oligo package attaching phenodata for HuGene2.0 ST array   Guest [guest]
  • [BioC] oligo package attaching phenodata for HuGene2.0 ST array   James W. MacDonald
    • [BioC] oligo package attaching phenodata for HuGene2.0 ST array   Jia, Li (NIH/NCI) [C]
  • [BioC] oligo package attaching phenodata for HuGene2.0 ST array   James W. MacDonald
• [BioC] TopGO 0 nontrivial nodes   Dario Strbenac
  • [BioC] TopGO 0 nontrivial nodes   Dario Strbenac
• [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
  • [BioC] Quickest way to convert IDs in a data frame?   James W. MacDonald
    • [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
      • [BioC] Quickest way to convert IDs in a data frame?   James W. MacDonald
      • [BioC] Quickest way to convert IDs in a data frame?   James W. MacDonald
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] Quickest way to convert IDs in a data frame?   James W. MacDonald
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] Quickest way to convert IDs in a data frame?   Marc Carlson
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] convert IDs in a data frame?   Hervé Pagès
      • [BioC] convert IDs in a data frame?   Marc Carlson
      • [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
      • [BioC] Quickest way to convert IDs in a data frame?   Marc Carlson
      • [BioC] Quickest way to convert IDs in a data frame?   Enrico Ferrero
      • [BioC] Quickest way to convert IDs in a data frame?   Marc Carlson
      • [BioC] Quickest way to convert IDs in a data frame?   Hervé Pagès
      • [BioC] Quickest way to convert IDs in a data frame?   Thomas Girke
• [BioC] bumphunter::matchGenes and all=TRUE   Anne Biton
  • [BioC] bumphunter::matchGenes and all=TRUE   Kasper Daniel Hansen
    • [BioC] bumphunter::matchGenes and all=TRUE   Harris A. Jaffee
      • [BioC] bumphunter::matchGenes and all=TRUE   Anne Biton
      • [BioC] bumphunter::matchGenes and all=TRUE   Harris A. Jaffee
      • [BioC] bumphunter::matchGenes and all=TRUE   Anne Biton
• [BioC] weird model design for DE analysis   Lorena Pantano
  • [BioC] weird model design for DE analysis   Michael Love
    • [BioC] weird model design for DE analysis   Lorena Pantano
  • [BioC] weird model design for DE analysis   Gordon K Smyth
    • [BioC] weird model design for DE analysis   Lorena Pantano
• [BioC] org.Hs.eg.db package loading issues   Guest [guest]
  • [BioC] org.Hs.eg.db package loading issues   Ekta Jain
    • [BioC] org.Hs.eg.db package loading issues   Jia, Li (NIH/NCI) [C]
  • [BioC] org.Hs.eg.db package loading issues   Dan Tenenbaum
    • [BioC] org.Hs.eg.db package loading issues   Jia, Li (NIH/NCI) [C]
• [BioC] Diffbind : use of controlBam   Rory Stark
  • [BioC] Diffbind : use of controlBam   Daniele Merico
    • [BioC] Diffbind : use of controlBam   Rory Stark
      • [BioC] Diffbind : use of controlBam   Daniele Merico
  • [BioC] Diffbind : use of controlBam   Rory Stark
• [BioC] Pathview with non-KEGG organisms?   Luo Weijun
• [BioC] Rsubread for paired end SOLID sequencing   Simon Coetzee
  • [BioC] Rsubread for paired end SOLID sequencing   Wei Shi
    • [BioC] Rsubread for paired end SOLID sequencing   Simon Coetzee
      • [BioC] Rsubread for paired end SOLID sequencing   Wei Shi
• [BioC] problem with installation package useR2013   Bartek [guest]
  • [BioC] problem with installation package useR2013   Dan Tenenbaum
• [BioC] issue on removing all NAs (UNANNOTATED) rows   Guest [guest]
  • [BioC] issue on removing all NAs (UNANNOTATED) rows   James W. MacDonald
• [BioC] DexSeq extracols option   Ioannis Vlachos
  • [BioC] DexSeq extracols option   Alejandro Reyes
    • [BioC] DexSeq extracols option   Ioannis Vlachos
    • [BioC] DexSeq extracols option   Ioannis Vlachos
• [BioC] Error in extracting genes from Goterms using GOStats package   Sandy [guest]
  • [BioC] Error in extracting genes from Goterms using GOStats package   James W. MacDonald
• [BioC] How to subtract the background from foreground values in GenePix files   John Velu [guest]
  • [BioC] How to subtract the background from foreground values in GenePix files   James W. MacDonald
• [BioC] About the state of KEGG-related packages   Enrico Ferrero
  • [BioC] About the state of KEGG-related packages   Marc Carlson
    • [BioC] About the state of KEGG-related packages   Enrico Ferrero
      • [BioC] About the state of KEGG-related packages   Calin Voichita
  • [BioC] About the state of KEGG-related packages   Luo Weijun
    • [BioC] About the state of KEGG-related packages   Enrico Ferrero
• [BioC] RNAseq data normalization without differential expression   Mete Civelek
  • [BioC] RNAseq data normalization without differential expression   Michael Love
    • [BioC] RNAseq data normalization without differential expression   Civelek, Mete
• [BioC] maskBAD package - Errors during creation of mask   Ron Rotkopf
• [BioC] miRNA prediction against a gene list   Martin Leonardo
• [BioC] Error converting SBML to graph Object using R SBML   Robin Philip
  • [BioC] Error converting SBML to graph Object using R SBML   Dan Tenenbaum
    • [BioC] Error converting SBML to graph Object using R SBML   Michael Lawrence
      • [BioC] Error converting SBML to graph Object using R SBML   Robin Philip
      • [BioC] Error converting SBML to graph Object using R SBML   Steve Lianoglou
• [BioC] How to handle the case a Affymetrix probe set ID mapped to multiple genes?   Feng Tian
  • [BioC] Fwd: How to handle the case a Affymetrix probe set ID mapped to multiple genes?   Levi Waldron
    • [BioC] Fwd: How to handle the case a Affymetrix probe set ID mapped to multiple genes?   Levi Waldron
      • [BioC] How to handle the case a Affymetrix probe set ID mapped to multiple genes?   Yuan Hao
      • [BioC] How to handle the case a Affymetrix probe set ID mapped to multiple genes?   Levi Waldron
• [BioC] rtracklayer error?   Janet Young
  • [BioC] rtracklayer problem on large number of GRanges   Janet Young
    • [BioC] rtracklayer problem on large number of GRanges   Janet Young
      • [BioC] rtracklayer problem on large number of GRanges   Michael Lawrence
      • [BioC] rtracklayer problem on large number of GRanges   Janet Young
      • [BioC] rtracklayer problem on large number of GRanges   Michael Lawrence
• [BioC] read.exon( )   Sanjana [guest]
• [BioC] ClusterProfiler Help   worah kuntal
• [BioC] rtracklayer carrying over query results   Janet Young
• [BioC] Limma removeBatchEffect   Mueller, Arne
  • [BioC] Limma removeBatchEffect   James W. MacDonald
• [BioC] HTqPCR normalization issue ?   alessandro.guffanti at genomnia.com
• [BioC] Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)   Olivier [guest]
  • [BioC] Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)   James W. MacDonald
    • [BioC] Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)   Olivier S.A.
      • [BioC] SVA: Removing batch effects without regards to differential expression   Mete Civelek
• [BioC] RIPSeeker multicore option not working fully?   Davis, Wade
  • [BioC] RIPSeeker multicore option not working fully?   Dan Tenenbaum
    • [BioC] RIPSeeker multicore option not working fully?   Yue Li

Last message date: Wed Jul 31 22:59:13 CEST 2013
Archived on: Thu Aug 1 07:19:23 CEST 2013

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