June 2013 Archives by thread

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Starting: Sat Jun 1 01:19:14 CEST 2013
Ending: Sun Jun 30 21:38:26 CEST 2013
Messages: 568

• [BioC] import gene annotations from genbank   Sean [guest]
  • [BioC] import gene annotations from genbank   Hans-Rudolf Hotz
• [BioC] DEXSeq troubles   Margaret Linan
  • [BioC] DEXSeq troubles   Alejandro Reyes
• [BioC] does contamination bother the normalization in transcriptome analysis   Maciej Jończyk
• [BioC] findOverlaps error   Reema Singh
  • [BioC] findOverlaps error   Martin Morgan
  • [BioC] findOverlaps error   Hervé Pagès
• [BioC] oligo package   Shahenda El-Naggar [guest]
  • [BioC] oligo package   Benilton Carvalho
  • [BioC] oligo package   Duval, Manuel
    • [BioC] oligo package   Benilton Carvalho
• [BioC] frmaTools library error :: makeVectorsAffyBatch() function   Tae-Hoon Chung
  • [BioC] frmaTools library error :: makeVectorsAffyBatch() function   Matthew McCall
• [BioC] Semantics of GenomicRanges gaps()   Hervé Pagès
  • [BioC] Semantics of GenomicRanges gaps()   Michael Lawrence
• [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
  • [BioC] DESeq /edgeR design problem for a small RNASeq   Simon Anders
    • [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Simon Anders
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Simon Anders
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Simon Anders
      • [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
  • [BioC] DESeq /edgeR design problem for a small RNASeq   Gordon K Smyth
    • [BioC] DESeq /edgeR design problem for a small RNASeq   Eduardo Andrés León
• [BioC] MAplot for both normalized and non-normalizes intensities   Paraskevi Dimoraga
• [BioC] using beadarray to process iscan expression data - error using readIllumina()   Darren Plant
• [BioC] Reading Affy CEL files   Ranjani R
  • [BioC] Reading Affy CEL files   James W. MacDonald
  • [BioC] Reading Affy CEL files   Sidders, Benjamin
• [BioC] Error in calculating P-values with Genefilter function   Brad Cattrysse [guest]
  • [BioC] [devteam-bioc] Error in calculating P-values with Genefilter function   Martin Morgan
  • [BioC] Error in calculating P-values with Genefilter function   James W. MacDonald
  • [BioC] Error in calculating P-values with Genefilter function   James W. MacDonald
    • [BioC] Error in calculating P-values with Genefilter function   Bradley Cattrysse
      • [BioC] Error in calculating P-values with Genefilter function   James W. MacDonald
      • [BioC] Error in calculating P-values with Genefilter function   Bradley Cattrysse
      • [BioC] Error in calculating P-values with Genefilter function   James W. MacDonald
      • [BioC] Error in calculating P-values with Genefilter function   Bradley Cattrysse
      • [BioC] Error in calculating P-values with Genefilter function   Steve Lianoglou
• [BioC] From location to get the SNP rs ID   Fabrice Tourre
  • [BioC] From location to get the SNP rs ID   Hervé Pagès
    • [BioC] From location to get the SNP rs ID   Fabrice Tourre
• [BioC] using beadarray or limma without spatial information   Sashank K.[guest]
  • [BioC] using beadarray or limma without spatial information   Wei Shi
• [BioC] rBiopaxParser error   suzy.stiegelmeyer at syngenta.com
  • [BioC] rBiopaxParser error   Dan Tenenbaum
    • [BioC] rBiopaxParser error   Frank Kramer
• [BioC] goseq and transcript length data   Tom [guest]
  • [BioC] goseq and transcript length data   Nadia Davidson
• [BioC] voom and RPKM for multi-species RNA-seq analysis   Julien Roux
• [BioC] Rsamtools: Realloc integer overflow?   Michael Lawrence
  • [BioC] Rsamtools: Realloc integer overflow?   Martin Morgan
    • [BioC] Rsamtools: Realloc integer overflow?   Hervé Pagès
      • [BioC] Rsamtools: Realloc integer overflow?   Martin Morgan
      • [BioC] Rsamtools: Realloc integer overflow?   Michael Lawrence
• [BioC] GWATools use in creating ncdf files   Stephanie M. Gogarten
  • [BioC] GWATools use in creating ncdf files   Sam Rose
    • [BioC] GWATools use in creating ncdf files   Stephanie M. Gogarten
      • [BioC] GWATools use in creating ncdf files   Sam Rose
      • [BioC] GWATools use in creating ncdf files   Stephanie M. Gogarten
      • [BioC] GWATools use in creating ncdf files   Sam Rose
• [BioC] RS-DBI driver error with org.Sc.sgd.db   Robert Castelo
  • [BioC] RS-DBI driver error with org.Sc.sgd.db   Marc Carlson
    • [BioC] RS-DBI driver error with org.Sc.sgd.db   Robert Castelo
      • [BioC] RS-DBI driver error with org.Sc.sgd.db   Marc Carlson
      • [BioC] RS-DBI driver error with org.Sc.sgd.db   Robert Castelo
• [BioC] preprocess core for quantile normalization   Yashwant Kumar [guest]
  • [BioC] preprocess core for quantile normalization   Tim Triche, Jr.
    • [BioC] preprocess core for quantile normalization   Tim Triche, Jr.
• [BioC] first time using combat   Johnson, William Evan
  • [BioC] first time using combat   Fernando Andrade
  • [BioC] first time using combat   Johnson, William Evan
• [BioC] Combat   Johnson, William Evan
• [BioC] GEOquery and Sample Subsets   Thomas H. Hampton
  • [BioC] GEOquery and Sample Subsets   Sean Davis
    • [BioC] GEOquery and Sample Subsets   Thomas H. Hampton
      • [BioC] GEOquery and Sample Subsets   Sean Davis
      • [BioC] GEOquery and Sample Subsets   Thomas H. Hampton
      • [BioC] GEOquery and Sample Subsets   Sean Davis
• [BioC] Problem when loading simpleaffy package   Michael Steeves
  • [BioC] Problem when loading simpleaffy package   Martin Morgan
• [BioC] Remove batch effects from RNA-seq data using edgeR and sva/ComBat   David O'Brien
  • [BioC] Remove batch effects from RNA-seq data using edgeR and sva/ComBat   Gordon K Smyth
    • [BioC] Remove batch effects from RNA-seq data using edgeR and sva/ComBat   Wang Peter
• [BioC] using a gtf file to map reads   Sam McInturf
  • [BioC] using a gtf file to map reads   Hans-Rudolf Hotz
  • [BioC] using a gtf file to map reads   Michael Lawrence
    • [BioC] using a gtf file to map reads   Sam McInturf
      • [BioC] using a gtf file to map reads   Michael Lawrence
      • [BioC] using a gtf file to map reads   Simon Anders
      • [BioC] using a gtf file to map reads   Michael Lawrence
      • [BioC] using a gtf file to map reads   Valerie Obenchain
      • [BioC] using a gtf file to map reads   Michael Love
      • [BioC] using a gtf file to map reads   Valerie Obenchain
• [BioC] graphite package   Mirza, Nasir
  • [BioC] graphite package   Dan Tenenbaum
• [BioC] Implications of design argument to limma::voom?   Ryan C. Thompson
  • [BioC] Implications of design argument to limma::voom?   Gordon K Smyth
    • [BioC] Implications of design argument to limma::voom?   Ryan C. Thompson
• [BioC] a question in merging sam files for DEXSeq   Chunjiang He
  • [BioC] a question in merging sam files for DEXSeq   Steve Lianoglou
  • [BioC] a question in merging sam files for DEXSeq   Simon Anders
• [BioC] edgeR MDS   Manoj Hariharan
  • [BioC] edgeR MDS   Gordon K Smyth
    • [BioC] edgeR MDS   Manoj Hariharan
• [BioC] using ComBat for protein data   Yashwant Kumar [guest]
• [BioC] cpm on normalised counts (was "DESeq normalisation strategy")   Davide Cittaro
• [BioC] Filtering is not recommended with LIMMA?   Gordon K Smyth
• [BioC] DEXSeq: PlotMA issues   Alejandro Reyes
• [BioC] beadarray - combining swath files   Darren
  • [BioC] beadarray - combining swath files   Mark Dunning
    • [BioC] beadarray - combining swath files   Darren Plant
      • [BioC] beadarray - combining swath files   Mark Dunning
      • [BioC] beadarray - combining swath files   Darren Plant
      • [BioC] beadarray - combining swath files   Mark Dunning
      • [BioC] beadarray - combining swath files   Darren Plant
      • [BioC] beadarray - combining swath files   Mark Dunning
      • [BioC] beadarray - combining swath files   Darren Plant
      • [BioC] beadarray - combining swath files   Darren Plant
• [BioC] Bioconductor Digest, Vol 124, Issue 5   Johnson, William Evan
  • [BioC] Bioconductor Digest, Vol 124, Issue 5   Hector Corrada Bravo
• [BioC] request on negative values after 'sva' correction   Johnson, William Evan
• [BioC] [DESeq] p-value vs adjusted p-value   lucia kwak
  • [BioC] [DESeq] p-value vs adjusted p-value   Steve Lianoglou
    • [BioC] [DESeq] p-value vs adjusted p-value   Davide Cittaro
      • [BioC] [DESeq] p-value vs adjusted p-value   lucia kwak
      • [BioC] [DESeq] p-value vs adjusted p-value   Simon Anders
      • [BioC] [DESeq] p-value vs adjusted p-value   Davide Cittaro
• [BioC] Detecting differential usage of introns from RNA-seq data.   Delasa Aghamirzaie
  • [BioC] Detecting differential usage of introns from RNA-seq data.   Alejandro Reyes
• [BioC] package not found: SequenceAnalysisData   Xiaolian Yuan
  • [BioC] package not found: SequenceAnalysisData   Dan Tenenbaum
    • [BioC] package not found: SequenceAnalysisData   Martin Morgan
      • [BioC] package not found: SequenceAnalysisData   Xiaolian Yuan
• [BioC] accounting for gene length with SeqGSEA   julie.leonard at syngenta.com
• [BioC] deicdeTest error   Chirag Gupta
• [BioC] PAIR files -- feature set table   FRANKLIN JOHNSON [guest]
  • [BioC] PAIR files -- feature set table   Benilton Carvalho
    • [BioC] PAIR files -- feature set table   Johnson, Franklin Theodore
      • [BioC] PAIR files -- feature set table   Benilton Carvalho
      • [BioC] PAIR files -- feature set table   Johnson, Franklin Theodore
      • [BioC] PAIR files -- feature set table   Johnson, Franklin Theodore
      • [BioC] PAIR files -- feature set table   Benilton Carvalho
      • [BioC] PAIR files -- feature set table   Johnson, Franklin Theodore
      • [BioC] PAIR files -- feature set table   Benilton Carvalho
      • [BioC] PAIR files -- feature set table   Benilton Carvalho
      • [BioC] PAIR files -- feature set table   Johnson, Franklin Theodore
• [BioC] No consensus among samples when sorted with t-stats - Need Help   Atul Kakrana
• [BioC] Error loading GO.db   Anne Deslattes Mays
  • [BioC] Error loading GO.db   Dan Tenenbaum
    • [BioC] Error loading GO.db   James W. MacDonald
      • [BioC] Error loading GO.db   Dan Tenenbaum
      • [BioC] Error loading GO.db   Martin Morgan
      • [BioC] Error loading GO.db   Ari Eszter
      • [BioC] Error loading GO.db   Martin Morgan
    • [BioC] Error loading GO.db   Anne Deslattes Mays
    • [BioC] Error loading GO.db   Dan Tenenbaum
• [BioC] Varied performance of readGappedAlignmentPairs function   Pan Du
  • [BioC] Varied performance of readGappedAlignmentPairs function   Hervé Pagès
    • [BioC] Varied performance of readGappedAlignmentPairs function   Michael Lawrence
      • [BioC] Varied performance of readGappedAlignmentPairs function   Hervé Pagès
• [BioC] detectionCall usefulness   Francisco Ortuno [guest]
  • [BioC] detectionCall usefulness   Pan Du
• [BioC] Problem in installing Rgraphviz   Heba [guest]
  • [BioC] Problem in installing Rgraphviz   Dan Tenenbaum
    • [BioC] Problem in installing Rgraphviz   Kasper Daniel Hansen
  • [BioC] Problem in installing Rgraphviz   Steve Lianoglou
    • [BioC] Problem in installing Rgraphviz   Kasper Daniel Hansen
• [BioC] interaction effects for DEXSeq   Mallon, Eamonn B. (Dr.)
  • [BioC] interaction effects for DEXSeq   Mallon, Eamonn B. (Dr.)
    • [BioC] interaction effects for DEXSeq   Mallon, Eamonn B. (Dr.)
  • [BioC] interaction effects for DEXSeq   Simon Anders
    • [BioC] interaction effects for DEXSeq   Mallon, Eamonn B. (Dr.)
    • [BioC] interaction effects for DEXSeq   Simon Anders
• [BioC] easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information   Gabriele Zoppoli
• [BioC] virtualArray package - Error while combing data sets   Atul Kakrana
• [BioC] GEOmetadb query to retrieve sample groups   Thomas H. Hampton
  • [BioC] GEOmetadb query to retrieve sample groups   Thomas H. Hampton
  • [BioC] GEOmetadb query to retrieve sample groups   Sean Davis
• [BioC] MEDIPS differential coverage   Sara Castelletti
• [BioC] About the DiffBind dba.count() crash problems   kentanaka at chiba-u.jp
  • [BioC] About the DiffBind dba.count() crash problems   Gordon Brown
• [BioC] Functions   Ipsitha [guest]
  • [BioC] Functions   James W. MacDonald
    • [BioC] Functions   Steve Lianoglou
      • [BioC] Functions   James W. MacDonald
      • [BioC] Functions   Steve Lianoglou
• [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Thomas Girke
  • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Cook, Malcolm
    • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Cook, Malcolm
    • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Thomas Girke
      • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Hervé Pagès
      • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Thomas Girke
      • [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes   Marc Carlson
• [BioC] inSilicoMerging and Limma   Ed Siefker
  • [BioC] inSilicoMerging and Limma   Ed Siefker
    • [BioC] inSilicoMerging and Limma   P.D. Moerland
• [BioC] Issue of installing the GLAD package   Aiden [guest]
  • [BioC] Issue of installing the GLAD package   Laurent Gatto
• [BioC] goseq and transcript length   Xulong Wang
• [BioC] DESEQ ANODEV : A time course study   Michael Breen
  • [BioC] DESEQ ANODEV : A time course study   Simon Anders
  • [BioC] DESEQ ANODEV : A time course study   Gordon K Smyth
    • [BioC] DESEQ ANODEV : A time course study   Michael Breen
  • [BioC] DESEQ ANODEV : A time course study   Michael Breen
    • [BioC] DESEQ ANODEV : A time course study   Ryan C. Thompson
      • [BioC] DESEQ ANODEV : A time course study   Michael Breen
      • [BioC] A time course study: using edgeR   Gordon K Smyth
• [BioC] pathview   Luo Weijun
• [BioC] Exonic part number of genes on the reverse strand   Conan [guest]
• [BioC] Huge variation in results among contrasts - Please Help!   Gordon K Smyth
• [BioC] How is LIMMA actually calculating the average expression value?   Garcia Orellana,Miriam
• [BioC] could not find function "makeProbePackage"   Merja Heinäniemi
  • [BioC] could not find function "makeProbePackage"   James W. MacDonald
• [BioC] Amazon EC2 MPI Cluster   Jonas Gylden
  • [BioC] Amazon EC2 MPI Cluster   Dan Tenenbaum
  • [BioC] Amazon EC2 MPI Cluster   Michael Steeves
    • [BioC] Question if DESeq can still be used after correction for T0?   Cor Lieftink [guest]
      • [BioC] Question if DESeq can still be used after correction for T0?   Simon Anders
      • [BioC] Question if DESeq can still be used after correction for T0?   Simon Anders
• [BioC] Error while executing ComBat from sva library in bioconductor   Johnson, William Evan
  • [BioC] Error while executing ComBat from sva library in bioconductor   francesco.brundu at gmail.com
• [BioC] edgeR - one way ANOVA, coef parameter interpretation in glmLRT()   Michal Okoniewski
  • [BioC] edgeR - one way ANOVA, coef parameter interpretation in glmLRT()   Mark Robinson
• [BioC] Rgraphviz::pieGlyph default values with warning   Cristobal Fresno Rodríguez
  • [BioC] Rgraphviz::pieGlyph default values with warning   Kasper Daniel Hansen
    • [BioC] Rgraphviz::pieGlyph default values with warning   Cristobal Fresno Rodríguez
      • [BioC] Rgraphviz::pieGlyph default values with warning   Kasper Daniel Hansen
• [BioC] installing biocLite('edgeR') issues   Marinus Pennings
  • [BioC] installing biocLite('edgeR') issues   Dan Tenenbaum
    • [BioC] installing biocLite('edgeR') issues   Marinus Pennings
      • [BioC] installing biocLite('edgeR') issues   Martin Morgan
• [BioC] Covariate for batch effect removal by ComBat   Atul Kakrana
  • [BioC] Covariate for batch effect removal by ComBat   Johnson, William Evan
• [BioC] Covariate for batch effect removal by ComBat with attachment   Atul Kakrana
• [BioC] How many biological replicates might suffice with Cox-Reid estimation in DESeq2 (or edgeR)?   Michael Muratet
  • [BioC] How many biological replicates might suffice with Cox-Reid estimation in DESeq2 (or edgeR)?   Michael Love
• [BioC] Error in makeOrgPackageFromNCBI   Chris Whelan
• [BioC] Gviz error with collapseTranscripts=TRUE   Stephanie M. Gogarten
  • [BioC] Gviz error with collapseTranscripts=TRUE   Hahne, Florian
  • [BioC] Gviz error with collapseTranscripts=TRUE   Hahne, Florian
• [BioC] Error when running Gene Set Variant Analysis (GSVA)   Lucas Santana dos Santos
  • [BioC] Error when running Gene Set Variant Analysis (GSVA)   Robert Castelo
    • [BioC] Error when running Gene Set Variant Analysis (GSVA)   Lucas Santana dos Santos
• [BioC] topTable coefficient   Ed Siefker
  • [BioC] topTable coefficient   Atul Kakrana
• [BioC] How is LIMMA actually calculating the average expression value   Gordon K Smyth
  • [BioC] How is LIMMA actually calculating the average expression value   Garcia Orellana,Miriam
    • [BioC] How is LIMMA actually calculating the average expression value   Gordon K Smyth
      • [BioC] How is LIMMA actually calculating the average expression value   Garcia Orellana,Miriam
      • [BioC] How is LIMMA actually calculating the average expression value   Gordon K Smyth
• [BioC] edgeR - GLM for multifactors   Alan Smith
  • [BioC] edgeR - GLM for multifactors   James W. MacDonald
• [BioC] return value used for filter amongst attributes, getBM(), biomaRt   James Perkins
• [BioC] DEXSeq, looking for a clever way for interpretation of results   Delasa Aghamirzaie
• [BioC] error to load the library affycoretools   Wang Peter
  • [BioC] error to load the library affycoretools   Sean Davis
• [BioC] DEXSeq: Problems trying to reproduce the example of the vignette   Simone
  • [BioC] DEXSeq: Problems trying to reproduce the example of the vignette   Wolfgang Huber
    • [BioC] DEXSeq: Problems trying to reproduce the example of the vignette   Simone
  • [BioC] DEXSeq: Problems trying to reproduce the example of the vignette   Ashu
    • [BioC] DEXSeq: Problems trying to reproduce the example of the vignette   Simone
• [BioC] HyperGtest interpretation   Maria [guest]
  • [BioC] HyperGtest interpretation   James W. MacDonald
• [BioC] DEXSeq: Factor   Margaret Linan
• [BioC] Rat St gene array 2.0   YBao
  • [BioC] Rat St gene array 2.0   James W. MacDonald
  • [BioC] Rat St gene array 2.0   Stephen Turner
• [BioC] [combat] par.priot=FALSE   Johnson, William Evan
• [BioC] Multi-factor multi-level analysis of RNAseq data   Alessandro Botton [guest]
  • [BioC] Multi-factor multi-level analysis of RNAseq data   Sam McInturf
    • [BioC] Multi-factor multi-level analysis of RNAseq data   Alessandro Botton
• [BioC] getGEO vs GEOmetadb   Jack Zhu
• [BioC] SRAdb package - problems   Jack Zhu
• [BioC] new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.   Hin-Tak Leung
• [BioC] lumiR error on *.idat and *.txt formated file   Joanne [guest]
  • [BioC] lumiR error on *.idat and *.txt formated file   Mark Dunning
• [BioC] do we need remove PCR duplicate before we look for DE genes   Wang Peter
  • [BioC] do we need remove PCR duplicate before we look for DE genes   Simon Anders
    • [BioC] do we need remove PCR duplicate before we look for DE genes   Lucia
      • [BioC] do we need remove PCR duplicate before we look for DE genes   Jonathan Cairns
• [BioC] TMM normalization of DESeq input data   Narges [guest]
  • [BioC] TMM normalization of DESeq input data   Ryan C. Thompson
• [BioC] optimizing VariantTools\' performance   Eric Foss [guest]
  • [BioC] optimizing VariantTools\' performance   Michael Lawrence
• [BioC] What is a good "control" for bacteria RNA-seq samples from a series of time points   Yanxiang Shi
  • [BioC] What is a good "control" for bacteria RNA-seq samples from a series of time points   Sam McInturf
    • [BioC] What is a good "control" for bacteria RNA-seq samples from a series of time points   Yanxiang Shi
      • [BioC] What is a good "control" for bacteria RNA-seq samples from a series of time points   Simon Anders
• [BioC] Error to install a package for Affymetrix data   chm chag
  • [BioC] Error to install a package for Affymetrix data   James W. MacDonald
    • [BioC] Error to install a package for Affymetrix data   Dario Strbenac
• [BioC] RIPSeeker package import error   Endre Sebestyen
• [BioC] Different number of differentially expressed genes after using ComBat in 'sva' for batch correction   Michaela Oswald
  • [BioC] Different number of differentially expressed genes after using ComBat in 'sva' for batch correction   Naomi Altman
• [BioC] ComBat function (sva) generates very low adjusted p.values for a big number of genes   Alexandra Popa
• [BioC] BioC 2013: Talks and Workshops   Martin Morgan
• [BioC] snapCGH and clonesinfo   Juliet Hannah
• [BioC] obtaining a complete global alignment via pairwiseAlignment   Robert K.Bradley [guest]
  • [BioC] obtaining a complete global alignment via pairwiseAlignment   Martin Morgan
    • [BioC] obtaining a complete global alignment via pairwiseAlignment   Robert K. Bradley
      • [BioC] obtaining a complete global alignment via pairwiseAlignment   Martin Morgan
      • [BioC] obtaining a complete global alignment via pairwiseAlignment   Hervé Pagès
      • [BioC] obtaining a complete global alignment via pairwiseAlignment   Robert K. Bradley
• [BioC] comparing seqnames   Murli Nair [guest]
  • [BioC] [devteam-bioc] comparing seqnames   Martin Morgan
    • [BioC] [devteam-bioc] comparing seqnames   Nair, Murlidharan T
    • [BioC] [devteam-bioc] comparing seqnames   Nair, Murlidharan T
• [BioC] help with ReportingTools   Abhishek Pratap
  • [BioC] help with ReportingTools   James W. MacDonald
    • [BioC] help with ReportingTools   Abhishek Pratap
      • [BioC] help with ReportingTools   Abhishek Pratap
• [BioC] cannot adjust legend in diffreport output   FRANKLIN JOHNSON [guest]
• [BioC] why could I only get two different expressed genes by Limma?   yongzi chen
  • [BioC] why could I only get two different expressed genes by Limma?   Atul Kakrana
• [BioC] cellHTS2 PlateList order problem   Hahne, Florian
• [BioC] carol white   carol white
• [BioC] GEOquery: incomplete feature data from GPL soft file   Renaud Gaujoux
• [BioC] using limma to analyze microarray data   xiayu [guest]
• [BioC] EMBO Practical Course on Bioinformatics and statistics for large-scale data: 17-22 Nov @ BGI   Wolfgang Huber
• [BioC] Missing as.list generic from AnnotationDbi?   Ryan C. Thompson
  • [BioC] Missing as.list generic from AnnotationDbi?   Ryan C. Thompson
• [BioC] ReportingTools: formatting html report   Abhishek Pratap
  • [BioC] ReportingTools: formatting html report   Jason Hackney
  • [BioC] ReportingTools: formatting html report   Gabriel Becker
• [BioC] diffbind, paired end reads   Rory Stark
  • [BioC] diffbind, paired end reads   Gordon Brown
    • [BioC] diffbind, paired end reads   Kasper Daniel Hansen
      • [BioC] diffbind, paired end reads   Gordon Brown
• [BioC] number of variable in svm plot   nofe [guest]
• [BioC] DEXSeq Question   Margaret Linan
• [BioC] DEXSeq Question <|------Ignore, I figured it out.   Margaret Linan
• [BioC] DESeq2 with multiple groups   Lorena Pantano
  • [BioC] DESeq2 with multiple groups   Michael Love
• [BioC] Finding the common ID from 3 objects or excels files in R   Nikul Soni
  • [BioC] Finding the common ID from 3 objects or excels files in R   Sean Davis
• [BioC] makePdInfoPackage for Primeview arrays   Max Kauer
  • [BioC] makePdInfoPackage for Primeview arrays   Benilton Carvalho
  • [BioC] makePdInfoPackage for Primeview arrays   cstrato
    • [BioC] makePdInfoPackage for Primeview arrays   Max Kauer
      • [BioC] makePdInfoPackage for Primeview arrays   James W. MacDonald
    • [BioC] SNP annotation in R   Ina Hoeschele
      • [BioC] SNP annotation in R   Valerie Obenchain
• [BioC] Regarding q-value   deepika lakhwani
• [BioC] Help with DMPFinder in minfi package   Srinivas Srikanth Manda
  • [BioC] Help with DMPFinder in minfi package   James W. MacDonald
    • [BioC] Help with DMPFinder in minfi package   Srinivas Srikanth Manda
      • [BioC] Help with DMPFinder in minfi package   James W. MacDonald
      • [BioC] Help with DMPFinder in minfi package   Srinivas Srikanth Manda
• [BioC] Create consensus fasta file from indexed Bam file   Jacques LE GOUIS [guest]
  • [BioC] [devteam-bioc] Create consensus fasta file from indexed Bam file   Hervé Pagès
    • [BioC] [devteam-bioc] Create consensus fasta file from indexed Bam file   Michael Lawrence
    • [BioC] [devteam-bioc] Create consensus fasta file from indexed Bam file   Jacques LEGOUIS
• [BioC] List of sequencing adapters   Julian Gehring
• [BioC] edgeR: very low p-value and very high variance within the group of replicates   valentina [guest]
  • [BioC] edgeR: very low p-value and very high variance within the group of replicates   Mark Robinson
  • [BioC] edgeR: very low p-value and very high variance within the group of replicates   Simon Anders
  • [BioC] edgeR: very low p-value and very high variance within the group of replicates   Gordon K Smyth
• [BioC] ReportingTools - trouble incorporating annotations   Sam McInturf
  • [BioC] ReportingTools - trouble incorporating annotations   James W. MacDonald
    • [BioC] ReportingTools - trouble incorporating annotations   Sam McInturf
      • [BioC] ReportingTools - trouble incorporating annotations   James W. MacDonald
      • [BioC] ReportingTools - trouble incorporating annotations   Gabriel Becker
      • [BioC] ReportingTools - trouble incorporating annotations   James W. MacDonald
      • [BioC] ReportingTools - trouble incorporating annotations   Gabriel Becker
      • [BioC] ReportingTools - trouble incorporating annotations   Sam McInturf
      • [BioC] ReportingTools - trouble incorporating annotations   Jason Hackney
      • [BioC] ReportingTools - trouble incorporating annotations   James W. MacDonald
• [BioC] error loading dba in DiffBind   Gordon Brown
  • [BioC] error loading dba in DiffBind   Lawson, Nathan
  • [BioC] error loading dba in DiffBind   Lawson, Nathan
  • [BioC] error loading dba in DiffBind   Gordon Brown
    • [BioC] error loading dba in DiffBind   Rory Stark
    • [BioC] error loading dba in DiffBind   Lawson, Nathan
• [BioC] Help with ensembl variation biomaRt query   William Noderer
• [BioC] p-value vs adjusted p-value in DEXSeq   Delasa Aghamirzaie
  • [BioC] p-value vs adjusted p-value in DEXSeq   Richard Friedman
  • [BioC] p-value vs adjusted p-value in DEXSeq   Simon Anders
    • [BioC] p-value vs adjusted p-value in DEXSeq   Delasa Aghamirzaie
• [BioC] Small RNA seq data analysis using DESeq   Vedran Franke
  • [BioC] Small RNA seq data analysis using DESeq   Wolfgang Huber
  • [BioC] Small RNA seq data analysis using DESeq   Simon Anders
• [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   James W. MacDonald
• [BioC] heatmap from limma output   Rao,Xiayu
  • [BioC] heatmap from limma output   James W. MacDonald
• [BioC] FeatureExpressionSet using list.files() in place of read.xysfiles()   Johnson, Franklin Theodore
  • [BioC] FeatureExpressionSet using list.files() in place of read.xysfiles()   Benilton Carvalho
    • [BioC] FeatureExpressionSet using list.files() in place of read.xysfiles()   Johnson, Franklin Theodore
      • [BioC] FeatureExpressionSet using list.files() in place of read.xysfiles()   Johnson, Franklin Theodore
      • [BioC] FeatureExpressionSet using list.files() in place of read.xysfiles()   Benilton Carvalho
• [BioC] getting a list of genomic sequences from a list of gene names   Eric Foss [guest]
• [BioC] convert data in to expression set   Nikul Soni
  • [BioC] convert data in to expression set   Jeremy Ng
• [BioC] Cell-type enrichment for gene expression   January Weiner
  • [BioC] Cell-type enrichment for gene expression   Tim Triche, Jr.
• [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] Useful information about Ensembl release 72 mart databases   Thomas Maurel
• [BioC] detecting gene-gene interactions from microarray data   Jeremy Ng
• [BioC] CummeRbund multiple cases   Himanshu Sharma
  • [BioC] CummeRbund multiple cases   Himanshu Sharma
    • [BioC] CummeRbund multiple cases   Delasa Aghamirzaie
• [BioC] heatmap-exprs error   Rao,Xiayu
  • [BioC] heatmap-exprs error   Wolfgang Huber
• [BioC] summarizeOverlaps: ambiguous method dispatch   Valerie Obenchain
• [BioC] ensembl to NCBI Mapping   Neeba Dijo
  • [BioC] ensembl to NCBI Mapping   James W. MacDonald
    • [BioC] How to retrieve all GO terms at level 5 as well as their annotated genes   Peter Davidsen
      • [BioC] How to retrieve all GO terms at level 5 as well as their annotated genes   Hervé Pagès
      • [BioC] How to retrieve all GO terms at level 5 as well as their annotated genes   Zadeh, Jenny Drnevich
      • [BioC] How to retrieve all GO terms at level 5 as well as their annotated genes   Hervé Pagès
• [BioC] Error to install a package for Affymetrix data‏   chm chag
  • [BioC] Error to install a package for Affymetrix data‏   James W. MacDonald
    • [BioC] Error to install a package for Affymetrix data‏   chm chag
      • [BioC] Error to install a package for Affymetrix data   Dan Tenenbaum
      • [BioC] Error to install a package for Affymetrix data   Steve Lianoglou
• [BioC] error in makeVectorsAffyBatch of frmaTools package   Ty Thomson
  • [BioC] error in makeVectorsAffyBatch of frmaTools package   Matthew McCall
    • [BioC] error in makeVectorsAffyBatch of frmaTools package   Ty Thomson
• [BioC] R sqllite referencing columns with :1 heading   barry [guest]
  • [BioC] R sqllite referencing columns with :1 heading   Hervé Pagès
• [BioC] TXNAME mapping   Murli [guest]
  • [BioC] TXNAME mapping   James W. MacDonald
  • [BioC] TXNAME mapping   Marc Carlson
    • [BioC] TXNAME mapping   Nair, Murlidharan T
    • [BioC] TXNAME mapping   Nair, Murlidharan T
    • [BioC] TXNAME mapping   Nair, Murlidharan T
• [BioC] Unexpected results of differential expression analysis   Laura [guest]
  • [BioC] Unexpected results of differential expression analysis   Wolfgang Huber
• [BioC] Error: IdeogramTrack (Gviz)   Tim Smith
  • [BioC] Error: IdeogramTrack (Gviz)   Steve Lianoglou
• [BioC] rsbml package installation error   Stefan Gries
  • [BioC] rsbml package installation error   Michael Breen
  • [BioC] rsbml package installation error   Michael Lawrence
    • [BioC] rsbml package installation error   Stefan Gries
• [BioC] DEXSeq output table   Mariana [guest]
• [BioC] edgeR ANOVA testing   Michael Breen
  • [BioC] edgeR ANOVA testing   Michael Breen
    • [BioC] edgeR ANOVA testing   Gordon K Smyth
• [BioC] romer implementation in edgeR   julie.leonard at syngenta.com
• [BioC] ERCC spike-in probes in   Brian Abraham [guest]
  • [BioC] ERCC spike-in probes in   James W. MacDonald
    • [BioC] ERCC spike-in probes in   James W. MacDonald
      • [BioC] ERCC spike-in probes in   Hooiveld, Guido
      • [BioC] ERCC spike-in probes in   Brian J. Abraham
      • [BioC] ERCC spike-in probes in   James W. MacDonald
• [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
  • [BioC] Repeated Measures mRNA expression analysis   Mike Love
  • [BioC] Repeated Measures mRNA expression analysis   Gordon K Smyth
    • [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
      • [BioC] Repeated Measures mRNA expression analysis   Gordon K Smyth
      • [BioC] Repeated Measures mRNA expression analysis   Charles Determan Jr
• [BioC] edgeR outlier question for version 3.0.8   Simon Melov
  • [BioC] edgeR outlier question for version 3.0.8   Gordon K Smyth
• [BioC] merging GRange objects   Murli [guest]
  • [BioC] merging GRange objects   Hervé Pagès
    • [BioC] merging GRange objects   Nair, Murlidharan T
      • [BioC] merging GRange objects   Hervé Pagès
      • [BioC] merging GRange objects   Nair, Murlidharan T
• [BioC] 'namespace:Biostrings' error when installing VariantAnnotation   Thomas Damm Als
  • [BioC] 'namespace:Biostrings' error when installing VariantAnnotation   Steve Lianoglou
  • [BioC] 'namespace:Biostrings' error when installing VariantAnnotation   Steve Lianoglou
    • [BioC] 'namespace:Biostrings' error when installing VariantAnnotation   Martin Morgan
      • [BioC] 'namespace:Biostrings' error when installing VariantAnnotation   Thomas Damm Als
• [BioC] Study design in DEXSeq   António Domingues
• [BioC] GSEA for R   January Weiner
  • [BioC] GSEA for R   James W. MacDonald
  • [BioC] GSEA for R   Steve Lianoglou
    • [BioC] GSEA for R   January Weiner
  • [BioC] GSEA for R   Sylvain Brohée
• [BioC] illumina microarray analysis questions (limma and heatmap)   Rao,Xiayu
• [BioC] installing the bioconductor package in R 3.0   Kaiyin Zhong (Victor Chung)
  • [BioC] installing the bioconductor package in R 3.0   Dan Tenenbaum
    • [BioC] installing the bioconductor package in R 3.0   Kaiyin Zhong (Victor Chung)
      • [BioC] installing the bioconductor package in R 3.0   Kaiyin Zhong (Victor Chung)
      • [BioC] installing the bioconductor package in R 3.0   Dan Tenenbaum
      • [BioC] installing the bioconductor package in R 3.0   Steve Lianoglou
• [BioC] limma: tissue specific genes using voom   Jaaved Mohammed
  • [BioC] limma: tissue specific genes using voom   Gordon K Smyth
    • [BioC] limma: tissue specific genes using voom   Jaaved Mohammed
• [BioC] SeqGSEA estiGeneNBstat()   SeqGSEA-user [guest]
  • [BioC] SeqGSEA estiGeneNBstat()   Xi Wang
• [BioC] Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital & Harvard Medical School   Wittner, Ben, Ph.D.
• [BioC] How to format SWAN minfi data for bumphunter?   Lara Park [guest]
• [BioC] running roast with 6 samples in 2 groups   julie.leonard at syngenta.com
  • [BioC] running roast with 6 samples in 2 groups   Wu, Di
• [BioC] Pathview published in Bioinformatics   Luo Weijun
  • [BioC] Pathview published in Bioinformatics   Luo Weijun
    • [BioC] Pathview published in Bioinformatics   Luo Weijun
      • [BioC] Pathview published in Bioinformatics   Luo Weijun
  • [BioC] Pathview published in Bioinformatics   Luo Weijun
• [BioC] PREDA command does not work   Maria Arnedo Muñoz [guest]
  • [BioC] PREDA command does not work   Valerie Obenchain
• [BioC] htseq and dexseq   Andreia Fonseca
  • [BioC] htseq and dexseq   Steve Lianoglou
    • [BioC] htseq and dexseq   Andreia Fonseca
      • [BioC] htseq and dexseq   Andreia Fonseca
      • [BioC] htseq and dexseq   Simon Anders
      • [BioC] htseq and dexseq   Andreia Fonseca
      • [BioC] htseq and dexseq   Steve Lianoglou
      • [BioC] htseq and dexseq   Andreia Fonseca
• [BioC] \"mogene20sttranscriptcluster.db\" not available for installation   Yan Wang [guest]
  • [BioC] \"mogene20sttranscriptcluster.db\" not available for installation   James W. MacDonald
• [BioC] edgeR - ANOVA-like test for differential gene expression   Benedikt Drosse
  • [BioC] edgeR - ANOVA-like test for differential gene expression   Eduardo Andrés León
    • [BioC] edgeR - ANOVA-like test for differential gene expression   Benedikt Drosse
  • [BioC] edgeR - ANOVA-like test for differential gene expression   Ryan
  • [BioC] edgeR - ANOVA-like test for differential gene expression   Benedikt Drosse
• [BioC] test for differential expresssion   Rao,Xiayu
  • [BioC] test for differential expresssion   Michael Breen
  • [BioC] test for differential expresssion   Gordon K Smyth
    • [BioC] test for differential expresssion   Rao,Xiayu
      • [BioC] test for differential expresssion   Gordon K Smyth
• [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] read.ilmn() and variation between chips   Gordon K Smyth
• [BioC] edgeR multiple contrasts Vs. One test   Michael Breen
  • [BioC] edgeR multiple contrasts Vs. One test   Michael Breen
  • [BioC] edgeR multiple contrasts Vs. One test   Gordon K Smyth
    • [BioC] edgeR multiple contrasts Vs. One test   Naomi Altman
      • [BioC] edgeR multiple contrasts Vs. One test   Gordon K Smyth
    • [BioC] edgeR multiple contrasts Vs. One test   Michael Breen
• [BioC] Unable to \'standardise\' logtransformed dataset of contrasts using Mfuzz package   FRANKLIN JOHNSON [guest]
  • [BioC] Unable to \'standardise\' logtransformed dataset of contrasts using Mfuzz package   Matthias Futschik
• [BioC] xzfile() cannot open the connection, lzma encoder error 5.   Jose Guillen
• [BioC] Gviz import bed file for AnnotationTrack   Christopher DeBoever
• [BioC] comBat or PCA to adjust for hidden variables in qPCR data   shirley zhang
• [BioC] a question about chip normalization   Wang Peter
• [BioC] DEXSEq warning when using TRT functions   Eva Benito [guest]
  • [BioC] DEXSEq warning when using TRT functions   Simon Anders
    • [BioC] DEXSEq warning when using TRT functions   Simon Anders
• [BioC] Regarding extraction of 3' and 5'UTRs and exonic region of a gene.   Abdul Rawoof
  • [BioC] Regarding extraction of 3' and 5'UTRs and exonic region of a gene.   Hervé Pagès
    • [BioC] Regarding extraction of 3' and 5'UTRs and exonic region of a gene.   Abdul Rawoof
      • [BioC] Regarding extraction of 3' and 5'UTRs and exonic region of a gene.   Hervé Pagès
• [BioC] Limma design for single channel arrays with technical repeats   Giulio Di Giovanni
  • [BioC] Limma design for single channel arrays with technical repeats   Giulio Di Giovanni
    • [BioC] Limma design for single channel arrays with technical repeats   Gordon K Smyth
• [BioC] How to filter genes not expressed in all arrays using limma (single channel agilent microarray data)   Nori [guest]
• [BioC] lumiR returns ExpressionSet object instead of LumiBatch   Liu X [guest]
  • [BioC] lumiR returns ExpressionSet object instead of LumiBatch   Pan Du
    • [BioC] lumiR returns ExpressionSet object instead of LumiBatch   Xiao-yu Liu
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Victoria Svinti
• [BioC] RNA-seq: interaction effect with DESeq   galeb abu-ali
  • [BioC] RNA-seq: interaction effect with DESeq   galeb abu-ali
• [BioC] problems running DEXseq   Diya
  • [BioC] problems running DEXseq   Wolfgang Huber
    • [BioC] problems running DEXseq   Steve Lianoglou
      • [BioC] problems running DEXseq   Steve Lianoglou
  • [BioC] problems running DEXseq   Simon Anders
• [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differential proteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Tom Wenseleers
  • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Gordon K Smyth
    • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Wang Peter
      • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Tom Wenseleers
    • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Tom Wenseleers
      • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Gordon K Smyth
      • [BioC] Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixed models for RNAseq data   Tom Wenseleers
• [BioC] pulling out specific lines from a bam file   Eric Foss [guest]
  • [BioC] pulling out specific lines from a bam file   Martin Morgan
• [BioC] targets frame   FRANKLIN JOHNSON [guest]
• [BioC] Gene expression clustering using several dependent samples   Moritz Kebschull

Last message date: Sun Jun 30 21:38:26 CEST 2013
Archived on: Sun Jun 30 21:38:31 CEST 2013

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