May 2014 Archives by author

• Messages sorted by: [ thread ] [ subject ] [ date ]
• More info on this list...

Starting: Thu May 1 01:27:36 CEST 2014
Ending: Sat May 31 23:53:02 CEST 2014
Messages: 599

• [BioC] DESeq on CCAT identified chipseq peaks   QAMRA Aditi (GIS)
• [BioC] DESeq on CCAT identified chipseq peaks   QAMRA Aditi (GIS)
• [BioC] DESeq on CCAT identified chipseq peaks   QAMRA Aditi (GIS)
• [BioC] DESeq2 vs. DiffBind DESeq2   QAMRA Aditi (GIS)
• [BioC] DESeq on CCAT identified chipseq peaks   QAMRA Aditi (GIS)
• [BioC] Allele-specific copy numbers using 450K Illumina methylation microarrays   Aaerp
• [BioC] Error when trying to normalize human Exon arrays (pd.huex.1.0.st.v2)   Aaerp
• [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)   Simon Anders
• [BioC] DESeq2 Regularised Log for Clustering of Genes   Simon Anders
• [BioC] DESeq on CCAT identified chipseq peaks   Simon Anders
• [BioC] DESeq vs DESeq2 have different DEGs results   Simon Anders
• [BioC] DEseq error   Simon Anders
• [BioC] DESeq2: up- and down-regulated genes   Simon Anders
• [BioC] DESeq2 - precisions about interaction and fold change calculation   Simon Anders
• [BioC] DESeq2: up- and down-regulated genes   Simon Anders
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Simon Anders
• [BioC] base R and genefilter have opposite definitions of anyNA()   Sonali Arora
• [BioC] Problem with DESeq : \"Error in FUN(newX[, i], ...) : could not find function \"locfunc\"\"   Camille BENOIST
• [BioC] Is this edgeR code OK?   Bernardo Bello
• [BioC] Please revise this edgeR code   Bernardo Bello
• [BioC] QQ plot 450k data   John Blischak
• [BioC] using duplicateCorrelation with limma+voom for RNA-seq data   John Blischak
• [BioC] Package qvalue - can it be installed without TCL-TK support?   John Blischak
• [BioC] using duplicateCorrelation with limma+voom for RNA-seq data   John Blischak
• [BioC] WGCNA on heterogeneous RNA-seq   Panos Bolan
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Caleb Bostwick
• [BioC] Help with aroma.light install   Luca Braglia
• [BioC] Gene expression analysis with edgeR with a large, nested design matrix   Ulrich Braunschweig
• [BioC] Combat Continuous   Michael Breen
• [BioC] Combat Continuous   Michael Breen
• [BioC] Combat Continuous   Michael Breen
• [BioC] Combat Continuous   Michael Breen
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Silav Bremos
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Silav Bremos
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Silav Bremos
• [BioC] limma small vs large number of samples   Giovanni Bucci
• [BioC] limma small vs large number of samples   Giovanni Bucci
• [BioC] limma vs t-test   Giovanni Bucci
• [BioC] limma and t-test, third time's a charm   Giovanni Bucci
• [BioC] limma vs t-test   Giovanni Bucci
• [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization   Stefanie Busch
• [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization   Stefanie Busch
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] snpStats reference allele used in genetic associations?   Vincent Carey
• [BioC] Creating a package   Vincent Carey
• [BioC] hg 19 Gene list   Marc Carlson
• [BioC] UCSC data anomaly in 50638 transcript(s): the cds cumulative length is   Marc Carlson
• [BioC] [devteam-bioc] loading/accessing older GO.db and org.Hs.eg.db data   Marc Carlson
• [BioC] Error DEXSeq   Roberta Carriero
• [BioC] oligo package - Unable to read HT-U133A CEL files   Benilton Carvalho
• [BioC] Error when trying to normalize human Exon arrays (pd.huex.1.0.st.v2)   Benilton Carvalho
• [BioC] problems installing VariantFiltering package   Robert Castelo
• [BioC] narrowpeaks profMatrix rangeval error   Robert Chase
• [BioC] mr.edgeR tests in MEDIPS package   Lukas Chavez
• [BioC] Connectons-nous sur LinkedIn   BEN HAMDA Cherif
• [BioC] Draft support for HTA 2.0 with oligo   Netta Mendelson Cohen
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Cook, Malcolm
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Cook, Malcolm
• [BioC] GEOquery error   Sean Davis
• [BioC] GEOquery error   Sean Davis
• [BioC] GEOquery error   Sean Davis
• [BioC] Adding annotations to GSE datasets   Sean Davis
• [BioC] Adding annotations to GSE datasets   Sean Davis
• [BioC] Adding annotations to GSE datasets   Sean Davis
• [BioC] Adding annotations to GSE datasets   Sean Davis
• [BioC] Adding annotations to GSE datasets   Sean Davis
• [BioC] Package "makecdfenv"   Romain Desert
• [BioC] Package "makecdfenv"   Romain Desert
• [BioC] reading CapitalBio corp microarray data with read.myimages   Romain Desert
• [BioC] [devteam-bioc] readGAlignmentPairs perfromace issue   Phil East
• [BioC] Error when loading biocLite.R via Rscript   David Eby
• [BioC] Error when loading biocLite.R via Rscript   David Eby
• [BioC] limma: design for paired data with multiple time points   Jonathan Ellis
• [BioC] limma: design for paired data with multiple time points   Jonathan Ellis
• [BioC] DE analysis with reference transcriptome   Nicole Ertl
• [BioC] Instance type at Bioconductor - Cloud AMI   Rohmatul Fajriyah
• [BioC] Instance type at Bioconductor - Cloud AMI   Rohmatul Fajriyah
• [BioC] Instance type at Bioconductor - Cloud AMI   Rohmatul Fajriyah
• [BioC] Instance type at Bioconductor - Cloud AMI   Rohmatul Fajriyah
• [BioC] Instance type at Bioconductor - Cloud AMI   Rohmatul Fajriyah
• [BioC] GEOquery error   Royce W. Fletcher
• [BioC] DESeq/DESeq normalization on different experiments   Gilgi Friedlander
• [BioC] biomaRt mapping id RP5-1043L13.1   Iain Gallagher
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Giuseppe Gallone
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Giuseppe Gallone
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Giuseppe Gallone
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Giuseppe Gallone
• [BioC] CellMix package use with own data matrix   Renaud Gaujoux
• [BioC] Gene expression and multivariables   Paul Geeleher
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Julian Gehring
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Julian Gehring
• [BioC] Installation of SomaticSignatures   Julian Gehring
• [BioC] information retrieval from pubmed   Julian Gehring
• [BioC] information retrieval from pubmed   Julian Gehring
• [BioC] information retrieval from pubmed   Julian Gehring
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Julian Gehring
• [BioC] Looping over entries of a GRanges object   Julian Gehring
• [BioC] Looping over entries of a GRanges object   Julian Gehring
• [BioC] Looping over entries of a GRanges object   Julian Gehring
• [BioC] DESeq2 transcript level   Thomas Girke
• [BioC] ComBat:RT-PCR Data   Giuliano
• [BioC] How to explain lumi expression values   Varshna Goelela
• [BioC] Problem CummeRbund   Loyal A. Goff
• [BioC] Problem CummeRbund   Loyal A. Goff
• [BioC] Problem CummeRbund   Loyal A. Goff
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Miss Agnieszka Aleksandra Golicz
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Miss Agnieszka Aleksandra Golicz
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Miss Agnieszka Aleksandra Golicz
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Miss Agnieszka Aleksandra Golicz
• [BioC] edgeR calcNormFactors for paired counts   Christopher T Gregg
• [BioC] edgeR calcNormFactors for paired counts   Christopher T Gregg
• [BioC] edgeR calcNormFactors for paired counts   Christopher T Gregg
• [BioC] Gviz AlignmentTrack - Consistent y-scales   Hahne, Florian
• [BioC] New error in Gviz   Hahne, Florian
• [BioC] gviz data track (heatmap) and title panel questions   Hahne, Florian
• [BioC] New error in Gviz   Hahne, Florian
• [BioC] gviz data track (heatmap) and title panel questions   Hahne, Florian
• [BioC] gviz data track (heatmap) and title panel questions   Hahne, Florian
• [BioC] displaying coverage RNAseq Gviz   Hahne, Florian
• [BioC] Displaying very deep coverage in Gviz   Hahne, Florian
• [BioC] displaying coverage RNAseq Gviz   Hahne, Florian
• [BioC] Displaying very deep coverage in Gviz   Hahne, Florian
• [BioC] GViz Annotation Track Stacking   Hahne, Florian
• [BioC] Gviz Incorrect Labels on Features   Hahne, Florian
• [BioC] Rgraphviz compilation error   Kasper Daniel Hansen
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Kasper Daniel Hansen
• [BioC] How to do a Vlookup-type function using a value range   Kasper Daniel Hansen
• [BioC] error in loading minfi package   Kasper Daniel Hansen
• [BioC] smoothing function in bumphunter in minfi   Kasper Daniel Hansen
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Kasper Daniel Hansen
• [BioC] error on loading ratioConvert() in minfi   Kasper Daniel Hansen
• [BioC] error on loading ratioConvert() in minfi   Kasper Daniel Hansen
• [BioC] DESeq2 transcript level   Yuan Hao
• [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14   Tom Harrop
• [BioC] RNA-seq pathway analysis in Canis familiaris   Jessica Perry Hekman
• [BioC] RNA-seq pathway analysis in Canis familiaris   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Problem running summarizeOverlaps()   Jessica Perry Hekman
• [BioC] Looping over entries of a GRanges object   Brian Herb
• [BioC] DESeq2 dispersion estimate gets stuck   Carl Herrmann
• [BioC] Gviz AnnotationTrack - Consistent y-scales   Aliaksei Holik
• [BioC] Gviz AlignmentTrack - Consistent y-scales   Aliaksei Holik
• [BioC] minfi, bumphunter + complex experimental design, and 3 other 450K queries   Hooiveld, Guido
• [BioC] total count filter cutoff   Wolfgang Huber
• [BioC] Course "CSAMA 2014" Computational Statistics for Genome Biology   Wolfgang Huber
• [BioC] genefilter vs limma - many probes filtered   Wolfgang Huber
• [BioC] genefilter vs limma - many probes filtered   Wolfgang Huber
• [BioC] in-group missing arrayQualityMetrics()   Wolfgang Huber
• [BioC] DESeq vs DESeq2 have different DEGs results   Catalina Aguilar Hurtado
• [BioC] DESeq vs DESeq2 have different DEGs results   Catalina Aguilar Hurtado
• [BioC] DESeq vs DESeq2 have different DEGs results   Catalina Aguilar Hurtado
• [BioC] DESeq vs DESeq2 have different DEGs results   Catalina Aguilar Hurtado
• [BioC] DESeq vs DESeq2 have different DEGs results   Catalina Aguilar Hurtado
• [BioC] Differences between limma voom E values and edgeR cpm values?   John Brothers II
• [BioC] How to do a Vlookup-type function using a value range   Harris A. Jaffee
• [BioC] hg 19 Gene list   chris Jhon
• [BioC] Gene expression and multivariables   chris Jhon
• [BioC] Gene expression and multivariables   chris Jhon
• [BioC] error on loading ratioConvert() in minfi   Jia, Li (NIH/NCI) [C]
• [BioC] error on loading ratioConvert() in minfi   Jia, Li (NIH/NCI) [C]
• [BioC] combat error message   Johnson, William Evan
• [BioC] Combat Continuous   Johnson, William Evan
• [BioC] ComBat - stuck please help!   Johnson, William Evan
• [BioC] ComBat:RT-PCR Data   Johnson, William Evan
• [BioC] granges() method for GenomicRanges objects akin to ranges()...   Johnston, Jeffrey
• [BioC] genefilter vs limma - many probes filtered   Marcin Jakub Kamiński
• [BioC] total count filter cutoff   Mahnaz Kiani
• [BioC] How to do Affy ST array analysis   Bernd Klaus
• [BioC] How to do Affy ST array analysis   Bernd Klaus
• [BioC] design matrix paired data   Bernd Klaus
• [BioC] design matrix paired data   Bernd Klaus
• [BioC] Error using the id function of ShortReadQ object   Bernd Klaus
• [BioC] using duplicateCorrelation with limma+voom for RNA-seq data   Bernd Klaus
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Bernd Klaus
• [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization   Pekka Kohonen
• [BioC] edgeR GLM using factor that varies for each gene   Daniel Lang
• [BioC] Combat Continuous   Peter Langfelder
• [BioC] Combat Continuous   Peter Langfelder
• [BioC] combat error message   Peter Langfelder
• [BioC] combat error message   Peter Langfelder
• [BioC] ComBat crash/problem   Peter Langfelder
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Peter Langfelder
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Michael Lawrence
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Michael Lawrence
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Michael Lawrence
• [BioC] error when coercing GenomeData to RangedData: 'no method or default for coercing “XStringViews” to “RangedData”'   Michael Lawrence
• [BioC] Newcommers question on subsetting IRangesList   Michael Lawrence
• [BioC] GenomicFeatures::makeTranscriptDbFromUCSC broken?   Michael Lawrence
• [BioC] Looping over entries of a GRanges object   Michael Lawrence
• [BioC] Looping over entries of a GRanges object   Michael Lawrence
• [BioC] Looping over entries of a GRanges object   Michael Lawrence
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Michael Lawrence
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Michael Lawrence
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Michael Lawrence
• [BioC] DataFrame(..., check.names=F); colnames change when assign data using '[[', not when using '[,]'   Michael Lawrence
• [BioC] Replacing GRanges mcol makes it inaccessible   Michael Lawrence
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Michael Lawrence
• [BioC] Best way of presenting "absolute" expression values (edgeR)   Sindre Lee
• [BioC] Database of known secretory protein coding human genes   Sindre Lee
• [BioC] DESeq2 stuck running   Mingfeng Li
• [BioC] DESeq2 stuck running   Mingfeng Li
• [BioC] DESeqs two-factor two-level, interaction is interested   Shucong Li
• [BioC] fail to load BSgenome.Hsapiens.UCSC.hg19   Yue Li
• [BioC] fail to load BSgenome.Hsapiens.UCSC.hg19   Yue Li
• [BioC] information retrieval from pubmed   Steve Lianoglou
• [BioC] limma vs t-test   Steve Lianoglou
• [BioC] Warning message while trying to install Bioconductor   Steve Lianoglou
• [BioC] mr.edgeR tests in MEDIPS package   Matthias Lienhard
• [BioC] Unable to load 'xps' library   Lili, Loukia
• [BioC] Unable to load 'xps' library - for Windows 7   Lili, Loukia
• [BioC] edgeR: dispersion estimation   Yanzhu Lin
• [BioC] DESeq2 : interactions ?   Michael Love
• [BioC] DESeq2 : interactions ?   Michael Love
• [BioC] Problem with DESeq : \"Error in FUN(newX[, i], ...) : could not find function \"locfunc\"\"   Michael Love
• [BioC] phyloseq/DESeq gives negative transformed values   Michael Love
• [BioC] phyloseq/DESeq gives negative transformed values   Michael Love
• [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)   Michael Love
• [BioC] Bioc mailing list captcha image down   Michael Love
• [BioC] DESeq2 with data containing 3 factors or more and outlier detection   Michael Love
• [BioC] DESeq2 Regularised Log for Clustering of Genes   Michael Love
• [BioC] DESeq2 transcript level   Michael Love
• [BioC] DESeq2 transcript level   Michael Love
• [BioC] DESeq2 stuck running   Michael Love
• [BioC] DESeq2 dispersion estimate gets stuck   Michael Love
• [BioC] DESeq2 stuck running   Michael Love
• [BioC] DESeq2 stuck running   Michael Love
• [BioC] DESeq2 Regularised Log for Clustering of Genes   Michael Love
• [BioC] DESeq2   Michael Love
• [BioC] DEXseq ignoreRank   Michael Love
• [BioC] DEXseq ignoreRank   Michael Love
• [BioC] DESeq2 stuck running   Michael Love
• [BioC] DESeq2 dispersion estimate gets stuck   Michael Love
• [BioC] DESeq2 stuck running   Michael Love
• [BioC] DESeq vs DESeq2 have different DEGs results   Michael Love
• [BioC] DESeqs two-factor two-level, interaction is interested   Michael Love
• [BioC] DESeqs two-factor two-level, interaction is interested   Michael Love
• [BioC] DESeq vs DESeq2 have different DEGs results   Michael Love
• [BioC] DESeq vs DESeq2 have different DEGs results   Michael Love
• [BioC] base R and genefilter have opposite definitions of anyNA()   Michael Love
• [BioC] DESeq vs DESeq2 have different DEGs results   Michael Love
• [BioC] DESeq/DESeq normalization on different experiments   Michael Love
• [BioC] Error: could not find function "plotPCA"   Michael Love
• [BioC] DE analysis with reference transcriptome   Michael Love
• [BioC] DESeq2: up- and down-regulated genes   Michael Love
• [BioC] DESeq2 - precisions about interaction and fold change calculation   Michael Love
• [BioC] DESeq2: up- and down-regulated genes   Michael Love
• [BioC] DESeq2: up- and down-regulated genes   Michael Love
• [BioC] Normalising both Affy mogene 1.0 and 1.1 together   Joel Ma
• [BioC] GEOquery error   James W. MacDonald
• [BioC] error in installing \"genefilter\"   James W. MacDonald
• [BioC] GEOquery error   James W. MacDonald
• [BioC] GEOquery error   James W. MacDonald
• [BioC] limma small vs large number of samples   James W. MacDonald
• [BioC] Sciplot: Increasing the width of bargraph and decreasing the sapce b/n groups   James W. MacDonald
• [BioC] getBM and sqldf error - no such table   James W. MacDonald
• [BioC] How to do a Vlookup-type function using a value range   James W. MacDonald
• [BioC] Paired comparisons in EdgeR   James W. MacDonald
• [BioC] design matrix paired data   James W. MacDonald
• [BioC] GenomicAlignments and QNAME collision   James W. MacDonald
• [BioC] pd.mirna.4.1   James W. MacDonald
• [BioC] Mapping gene symbols to gene names (org.Hs.eg.db?)   James W. MacDonald
• [BioC] error in loading a bioconductor package affy   James W. MacDonald
• [BioC] RNA-seq pathway analysis in Canis familiaris   James W. MacDonald
• [BioC] Normalising both Affy mogene 1.0 and 1.1 together   James W. MacDonald
• [BioC] QQ plot 450k data   James W. MacDonald
• [BioC] QQ plot 450k data   James W. MacDonald
• [BioC] limma: design for paired data with multiple time points   James W. MacDonald
• [BioC] QQ plot 450k data   James W. MacDonald
• [BioC] Package "makecdfenv"   James W. MacDonald
• [BioC] Package "makecdfenv"   James W. MacDonald
• [BioC] Error: could not find function "plotPCA"   James W. MacDonald
• [BioC] DE analysis with reference transcriptome   James W. MacDonald
• [BioC] Package "makecdfenv"   James W. MacDonald
• [BioC] Package "makecdfenv"   James W. MacDonald
• [BioC] Package "makecdfenv"   James W. MacDonald
• [BioC] biomaRt proxy issues   James W. MacDonald
• [BioC] Creating a package   James W. MacDonald
• [BioC] Error DEXSeq   Mallon, Eamonn B. (Dr.)
• [BioC] Error DEXSeq   Mallon, Eamonn B. (Dr.)
• [BioC] Error DEXSeq   Mallon, Eamonn B. (Dr.)
• [BioC] DEXseq ignoreRank   Marco Marconi
• [BioC] DEXseq ignoreRank   Marco Marconi
• [BioC] DEXseq ignoreRank   Marco Marconi
• [BioC] biomaRt mapping id RP5-1043L13.1   Thomas Maurel
• [BioC] edgeR, logFC calculation in factor combination   Mike Miller
• [BioC] edgeR, logFC calculation in factor combination   Mike Miller
• [BioC] edgeR, logFC calculation in factor combination   Mike Miller
• [BioC] SomaticSignatures   Martin Morgan
• [BioC] BioC 2014 Registration Open   Martin Morgan
• [BioC] [devteam-bioc] Howto achieve reverse complement in a ShortReadQ object   Martin Morgan
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Martin Morgan
• [BioC] a possible bug in the shortread packge   Martin Morgan
• [BioC] a possible bug in the shortread packge   Martin Morgan
• [BioC] Error when loading biocLite.R via Rscript   Martin Morgan
• [BioC] No access to bioconductor from a freshly installed R   Martin Morgan
• [BioC] a program to force fastq using pred+33 scoring system   Martin Morgan
• [BioC] a program to force fastq using pred+33 scoring system   Martin Morgan
• [BioC] Problem running summarizeOverlaps()   Martin Morgan
• [BioC] Problem running summarizeOverlaps()   Martin Morgan
• [BioC] Problem running summarizeOverlaps()   Martin Morgan
• [BioC] Problem running summarizeOverlaps()   Martin Morgan
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Martin Morgan
• [BioC] a program to force fastq using pred+33 scoring system   Martin Morgan
• [BioC] BiocParallel fatal error   Martin Morgan
• [BioC] Bioc 2014: reduced hotel rates   Martin Morgan
• [BioC] RNA-Seq vs. Microarray   Willemijn van Mossevelde
• [BioC] How to do Affy ST array analysis   Ninni Nahm
• [BioC] How to do Affy ST array analysis   Ninni Nahm
• [BioC] design matrix paired data   Ninni Nahm
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Sigve Nakken
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Sigve Nakken
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Sigve Nakken
• [BioC] information retrieval from pubmed   Nick
• [BioC] information retrieval from pubmed   Nick
• [BioC] BHC appears to be broken   OLIVER, DAVID
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Valerie Obenchain
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] Multi-sample VCF file and filterVcf   Valerie Obenchain
• [BioC] [devteam-bioc] readGAlignmentPairs perfromace issue   Valerie Obenchain
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Valerie Obenchain
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] DEXSeqDataSet   Hatice Ulku Osmanbeyoglu
• [BioC] Limma design code with technical replicates, paired samples and two factors   Otto, Benjamin
• [BioC] Limma design code with technical replicates, paired samples and two factors   Otto, Benjamin
• [BioC] question about how to understand exon usage coefficient value   Ou, Jianhong
• [BioC] error when coercing GenomeData to RangedData: 'no method or default for coercing “XStringViews” to “RangedData”'   Ludo Pagie
• [BioC] DataFrame(..., check.names=F); colnames change when assign data using '[[', not when using '[,]'   Ludo Pagie
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Hervé Pagès
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Hervé Pagès
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Hervé Pagès
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Hervé Pagès
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Hervé Pagès
• [BioC] fail to load BSgenome.Hsapiens.UCSC.hg19   Hervé Pagès
• [BioC] [devteam-bioc] readGAlignmentPairs perfromace issue   Hervé Pagès
• [BioC] UCSC data anomaly in 50638 transcript(s): the cds cumulative length is   Hervé Pagès
• [BioC] Replacing GRanges mcol makes it inaccessible   Shraddha Pai
• [BioC] Replacing GRanges mcol makes it inaccessible   Shraddha Pai
• [BioC] Gviz AlignmentTrack - Consistent y-scales   Lance Parsons
• [BioC] Gviz AlignmentTrack - Consistent y-scales   Lance Parsons
• [BioC] Displaying very deep coverage in Gviz   Lance Parsons
• [BioC] Displaying very deep coverage in Gviz   Lance Parsons
• [BioC] Displaying very deep coverage in Gviz   Lance Parsons
• [BioC] Gviz AlignmentTrack - Consistent y-scales   Lance Parsons
• [BioC] GViz Annotation Track Stacking   Lance Parsons
• [BioC] Displaying very deep coverage in Gviz   Lance Parsons
• [BioC] Gviz Incorrect Labels on Features   Lance Parsons
• [BioC] GViz Annotation Track Stacking   Lance Parsons
• [BioC] Gviz Incorrect Labels on Features   Lance Parsons
• [BioC] Creating a package   Matthew Robert Paul
• [BioC] Adding annotations to GSE datasets   Marcelo Pereira
• [BioC] Adding annotations to GSE datasets   Marcelo Pereira
• [BioC] Adding annotations to GSE datasets   Marcelo Pereira
• [BioC] Adding annotations to GSE datasets   Marcelo Pereira
• [BioC] Adding annotations to GSE datasets   Marcelo Pereira
• [BioC] a possible bug in the shortread packge   Wang Peter
• [BioC] a possible bug in the shortread packge   Wang Peter
• [BioC] how to change pred+33 to pred+44 in shortread   Wang Peter
• [BioC] a program to force fastq using pred+33 scoring system   Wang Peter
• [BioC] a program to force fastq using pred+33 scoring system   Wang Peter
• [BioC] a program to force fastq using pred+33 scoring system   Wang Peter
• [BioC] a program to force fastq using pred+33 scoring system   Wang Peter
• [BioC] oligo package - Unable to read HT-U133A CEL files   Steve Piccolo
• [BioC] Normalising both Affy mogene 1.0 and 1.1 together   Steve Piccolo
• [BioC] New error in Gviz   Miles Pufall
• [BioC] New error in Gviz   Miles Pufall
• [BioC] DESeq2 transcript level   Alicia R. Pérez-Porro
• [BioC] DESeq2 transcript level   Alicia R. Pérez-Porro
• [BioC] DESeq2 transcript level   Alicia R. Pérez-Porro
• [BioC] DESeq2 transcript level   Alicia R. Pérez-Porro
• [BioC] DESeq2 transcript level   Alicia R. Pérez-Porro
• [BioC] DESeq2: up- and down-regulated genes   Alicia R. Pérez-Porro
• [BioC] DESeq2: up- and down-regulated genes   Alicia R. Pérez-Porro
• [BioC] DESeq2: up- and down-regulated genes   Alicia R. Pérez-Porro
• [BioC] DESeq2: up- and down-regulated genes   Alicia R. Pérez-Porro
• [BioC] DESeq2: up- and down-regulated genes   Alicia R. Pérez-Porro
• [BioC] HTqPCR bug in geometric mean normalization   Johannes Rainer
• [BioC] DESeq2 transcript level   Rao,Xiayu
• [BioC] biomaRt proxy issues   Bill Raynor
• [BioC] biomaRt proxy issues   Raynor, Bill
• [BioC] DEXSeqDataSet   Alejandro Reyes
• [BioC] DEXSeqDataSet   Alejandro Reyes
• [BioC] DEXSeq design formula   Alejandro Reyes
• [BioC] Question about DEXSeq, DESeq, and pasilla   Alejandro Reyes
• [BioC] Error DEXSeq   Alejandro Reyes
• [BioC] Error DEXSeq   Alejandro Reyes
• [BioC] Error DEXSeq   Alejandro Reyes
• [BioC] Error DEXSeq   Alejandro Reyes
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] Fwd: adjusted P-values   Martin Rijlaarsdam
• [BioC] Fwd: adjusted P-values   Martin Rijlaarsdam
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] gviz data track (heatmap) and title panel questions   Martin Rijlaarsdam
• [BioC] QQ plot 450k data   Martin Rijlaarsdam
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Juergen Rose
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Juergen Rose
• [BioC] limma: percent of variance explained   Julien Roux
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Ryan
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Ryan
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Ryan
• [BioC] how to calculate gene length to be used in rpkm() in edgeR   Ryan
• [BioC] Paired comparisons in EdgeR   Ryan
• [BioC] featureCounts segfault   Ryan
• [BioC] Limma design code with technical replicates, paired samples and two factors   Ryan
• [BioC] using duplicateCorrelation with limma+voom for RNA-seq data   Ryan
• [BioC] DESeq/DESeq normalization on different experiments   Ryan
• [BioC] genefilter vs limma - many probes filtered   Ryan
• [BioC] edgeR calcNormFactors for paired counts   Ryan
• [BioC] edgeR calcNormFactors for paired counts   Ryan
• [BioC] combat error message   Natasha Sahgal
• [BioC] Paired comparisons in EdgeR   Jussi Salmi
• [BioC] Paired comparisons in EdgeR   Jussi Salmi
• [BioC] Paired comparisons in EdgeR   Jussi Salmi
• [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)   Schnell, Dan
• [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)   Schnell, Dan
• [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love) (Simon Anders)   Schnell, Dan
• [BioC] viewApply drops feature names; transfer names between lists   Chris Seidel
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] Feature request for Rsubread::featureCounts: read length adjustment   Wei Shi
• [BioC] featureCounts segfault   Wei Shi
• [BioC] featureCounts segfault   Wei Shi
• [BioC] ComBat - stuck please help!   Siddiq, Afshan
• [BioC] DEXSeq design formula   Simone
• [BioC] Mapping gene symbols to gene names (org.Hs.eg.db?)   Tim Smith
• [BioC] Mapping gene symbols to gene names (org.Hs.eg.db?)   Tim Smith
• [BioC] EdgeR: dispersion estimation   Gordon K Smyth
• [BioC] total count filter cutoff (edgeR)   Gordon K Smyth
• [BioC] How to explain lumi expression values   Gordon K Smyth
• [BioC] total count filter cutoff (edgeR)   Gordon K Smyth
• [BioC] how to calculate gene length to be used in rpkm() in edgeR   Gordon K Smyth
• [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization   Gordon K Smyth
• [BioC] edgeR: dispersion estimation   Gordon K Smyth
• [BioC] edgeR GLM using factor that varies for each gene   Gordon K Smyth
• [BioC] limma -roast: probe-level vs gene-level?   Gordon K Smyth
• [BioC] Best way of presenting "absolute" expression values (edgeR)   Gordon K Smyth
• [BioC] limma all by all   Gordon K Smyth
• [BioC] edgeR: dispersion estimation   Gordon K Smyth
• [BioC] limma: strange subsetting fit[, i] of "MArrayLM" object's design   Gordon K Smyth
• [BioC] limma: strange subsetting fit[, i] of MArrayLM object design   Gordon K Smyth
• [BioC] edgeR: dispersion estimation   Gordon K Smyth
• [BioC] edgeR, logFC calculation in factor combination   Gordon K Smyth
• [BioC] edgeR, logFC calculation in factor combination   Gordon K Smyth
• [BioC] limma: strange subsetting fit[, i] of MArrayLM object design   Gordon K Smyth
• [BioC] limma: percent of variance explained   Gordon K Smyth
• [BioC] limma vs t-test   Gordon K Smyth
• [BioC] genefilter vs limma - many probes filtered   Gordon K Smyth
• [BioC] Gene expression analysis with edgeR with a large, nested design matrix   Gordon K Smyth
• [BioC] Gene expression analysis with edgeR with a large, nested design matrix   Gordon K Smyth
• [BioC] limma vs t-test   Gordon K Smyth
• [BioC] edgeR, logFC calculation in factor combination   Gordon K Smyth
• [BioC] How to do a Vlookup-type function using a value range   Elena Sorokin
• [BioC] QuasR for miRNA   Michael Stadler
• [BioC] DESeq on CCAT identified chipseq peaks   Rory Stark
• [BioC] DESeq on CCAT identified chipseq peaks   Rory Stark
• [BioC] DESeq on CCAT identified chipseq peaks   Rory Stark
• [BioC] question about DiffBind   Rory Stark
• [BioC] DESeq on CCAT identified chipseq peaks   Rory Stark
• [BioC] ComBat:RT-PCR Data   Giuliano Stirparo
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Storey, John D.
• [BioC] DESeq2 Regularised Log for Clustering of Genes   Dario Strbenac
• [BioC] Sciplot: Increasing the width of bargraph and decreasing the sapce b/n groups   Roopa Subbaiaih
• [BioC] Error: could not find function "plotPCA"   Surles, Monique
• [BioC] Error: could not find function "plotPCA"   Surles, Monique
• [BioC] Error: could not find function "plotPCA"   Surles, Monique
• [BioC] limma: strange subsetting fit[, i] of "MArrayLM" object`s design matrix, also robust=TRUE and topTable   Maciek Sykulski
• [BioC] limma: strange subsetting fit[, i] of MArrayLM object design   Maciek Sykulski
• [BioC] Any Master in Bioinformatics?   Ibon Tamayo
• [BioC] color-coded arch intensity in ggbio   Bogdan Tanasa
• [BioC] color-coded arch intensity in ggbio   Bogdan Tanasa
• [BioC] UCSC data anomaly in 50638 transcript(s): the cds cumulative length is   Tarca, Adi
• [BioC] Instance type at Bioconductor - Cloud AMI   Dan Tenenbaum
• [BioC] Instance type at Bioconductor - Cloud AMI   Dan Tenenbaum
• [BioC] Instance type at Bioconductor - Cloud AMI   Dan Tenenbaum
• [BioC] Instance type at Bioconductor - Cloud AMI   Dan Tenenbaum
• [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14   Dan Tenenbaum
• [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14   Dan Tenenbaum
• [BioC] [Bioc-devel] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14   Dan Tenenbaum
• [BioC] Bioc mailing list captcha image down   Dan Tenenbaum
• [BioC] Error when loading biocLite.R via Rscript   Dan Tenenbaum
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Dan Tenenbaum
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Dan Tenenbaum
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Dan Tenenbaum
• [BioC] Unable to load 'xps' library   Dan Tenenbaum
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Dan Tenenbaum
• [BioC] Cannot Install ‘VariantTools’ Package on Mac   Dan Tenenbaum
• [BioC] Problem running summarizeOverlaps()   Ryan Thompson
• [BioC] featureCounts segfault   Ryan C. Thompson
• [BioC] graphite biopax conversion code?   Ryan C. Thompson
• [BioC] granges() method for GenomicRanges objects akin to ranges()...   Tim Triche, Jr.
• [BioC] granges() method for GenomicRanges objects akin to ranges()...   Tim Triche, Jr.
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Tim Triche, Jr.
• [BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...   Tim Triche, Jr.
• [BioC] Fwd: adjusted P-values   Tim Triche, Jr.
• [BioC] Adding annotations to GSE datasets   Tim Triche, Jr.
• [BioC] Displaying very deep coverage in Gviz   Tim Triche, Jr.
• [BioC] DESeq2   AROA SUÁREZ VEGA
• [BioC] mr.edgeR tests in MEDIPS package   Vining, Kelly
• [BioC] Convert phylogenetic tree to igraph   Sana Wajid
• [BioC] ComBat error message, thanks   Guan Wang
• [BioC] Can GAGE be used for transcript set pathway analysis   Luo Weijun
• [BioC] Pathview plot split by experiment condition   Luo Weijun
• [BioC] phyloseq/DESeq gives negative transformed values   Sophie Josephine Weiss
• [BioC] phyloseq/DESeq gives negative transformed values   Sophie Josephine Weiss
• [BioC] DESeq2 : interactions ?   Yvan Wenger
• [BioC] Package qvalue - can it be installed without TCL-TK support?   Pengcheng Yang
• [BioC] mfuzz problems   Assa Yeroslaviz
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Tengfei Yin
• [BioC] [devteam-bioc] GenomicRanges seqlengths problem   Tengfei Yin
• [BioC] color-coded arch intensity in ggbio   Tengfei Yin
• [BioC] CellMix package use with own data matrix   Zavodszky, Maria (GE Global Research)
• [BioC] segfault in rqubic   Zhang, Jitao David
• [BioC] DEseq error   Vineeta singh [guest]
• [BioC] DESeq on CCAT identified chipseq peaks   Aditi [guest]
• [BioC] GenomicRanges seqlengths problem   Agnieszka Golicz [guest]
• [BioC] No access to bioconductor from a freshly installed R   Alexandre Fort [guest]
• [BioC] NaNs in RMA normalization of GSE31312   Anders Ellern Bilgrau [guest]
• [BioC] Problem with DESeq : \"Error in FUN(newX[, i], ...) : could not find function \"locfunc\"\"   Benoist [guest]
• [BioC] limma -roast: probe-level vs gene-level?   Beth [guest]
• [BioC] Regarding hist() function in R   Bharat Upadrasta [guest]
• [BioC] biomaRt proxy issues   Bill Raynor [guest]
• [BioC] smoothing function in bumphunter in minfi   Brad Ruzicka [guest]
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Caleb Bostwick [guest]
• [BioC] reading qRT-PCR data   Chris [guest]
• [BioC] pd.mirna.4.1   Craig Johnson [guest]
• [BioC] edgeR GLM using factor that varies for each gene   Daniel Lang [guest]
• [BioC] getBM and sqldf error - no such table   David [guest]
• [BioC] runFastHeinz - Bug   Elangovan [guest]
• [BioC] segfault in rqubic   Eric Liaw [guest]
• [BioC] Warning message while trying to install Bioconductor   Felix Francis [guest]
• [BioC] snpStats reference allele used in genetic associations?   Francesca [guest]
• [BioC] DESeq/DESeq normalization on different experiments   Gilgi [guest]
• [BioC] limma vs t-test   Giovanni Bucci [guest]
• [BioC] limma vs t-test   Giovanni Bucci [guest]
• [BioC] t-test vs limma   Giovanni Bucci [guest]
• [BioC] limma & t-test, third time's a charm   Giovanni Bucci [guest]
• [BioC] loading/accessing older GO.db and org.Hs.eg.db data   Jonathan Mortensen [guest]
• [BioC] R-3.1.0: biocLite("vsn") removes all files in /   Juergen Rose [guest]
• [BioC] edgeR for RNA-seq: nested paired analysis with uneven groups   Laurence [guest]
• [BioC] EdgeR analysis   Mac449 [guest]
• [BioC] genefilter vs limma - many probes filtered   Marcin Kaminski [guest]
• [BioC] Creating a package   Matt Paul [guest]
• [BioC] DESeq2 stuck running   Mingfeng [guest]
• [BioC] combat error message   Natasha [guest]
• [BioC] How to do Affy ST array analysis   Ninni Nahm [guest]
• [BioC] design matrix paired data   Ninni Nahm [guest]
• [BioC] Problem CummeRbund   Petr [guest]
• [BioC] How to get all transcripts   Petr [guest]
• [BioC] readGAlignmentPairs perfromace issue   Phil East [guest]
• Cannot Install ‘VariantTools’ Package on Mac   Quine [guest]
• [BioC] BiocParallel fatal error   Rebecca [guest]
• [BioC] Error DEXSeq   Roberta Carriero [guest]
• [BioC] error in loading a bioconductor package affy   Sdg [guest]
• [BioC] DESeqs two-factor two-level, interaction is interested   Shawn [guest]
• [BioC] Installation of SomaticSignatures   Sigve Nakken [guest]
• [BioC] Multi-sample VCF file and filterVcf   Sigve Nakken [guest]
• [BioC] Howto achieve reverse complement in a ShortReadQ object   Tomas Bjorklund [guest]
• [BioC] Longest continuous sequence from multiple alignment   Tomas Bjorklund [guest]
• [BioC] Newcommers question on subsetting IRangesList   Tomas Bjorklund [guest]
• [BioC] Error using the id function of ShortReadQ object   Tomas Bjorklund [guest]
• [BioC] Gene expression analysis with edgeR with a large, nested design matrix   Uli Braunschweig [guest]
• [BioC] Gene Expression Meta Analysis   Vlad [guest]
• [BioC] edgeR: dispersion estimation   Yanzhu [guest]
• [BioC] error in loading minfi package   guest [guest]
• [BioC] error on loading ratioConvert() in minfi   guest [guest]
• [BioC] adjusted P-values   kaushal [guest]
• [BioC] error in installing \"genefilter\"   mahnaz Kiani [guest]
• [BioC] limma all by all   somnath bandyopadhyay
• [BioC] limma all by all   somnath bandyopadhyay
• [BioC] CellMix   somnath bandyopadhyay
• [BioC] DESeq2 - precisions about interaction and fold change calculation   samuel collombet
• [BioC] Unable to load 'xps' library - for Windows 7   cstrato
• [BioC] ChIPseeker: Error in annotatePeak   António domingues
• [BioC] ChIPseeker: Error in annotatePeak   António domingues
• [BioC] Gene Expression Meta Analysis   gokmenzararsiz at erciyes.edu.tr
• [BioC] DESeq2 stuck running   lmf.bill at gmail.com
• [BioC] minfi release 1.8   swarmqq at gmail.com
• [BioC] QQ plot 450k data   khadeeja ismail
• [BioC] QQ plot 450k data   khadeeja ismail
• [BioC] QQ plot 450k data   khadeeja ismail
• [BioC] Thalassiosira pseudonana   n omranian
• [BioC] Can GAGE be used for transcript set pathway analysis   sun
• [BioC] how to calculate gene length to be used in rpkm() in edgeR   shirley zhang
• [BioC] ComBat:RT-PCR Data   shirley zhang
• [BioC] Question about DEXSeq, DESeq, and pasilla   林宣佑

Last message date: Sat May 31 23:53:02 CEST 2014
Archived on: Mon Jun 2 12:14:32 CEST 2014

• Messages sorted by: [ thread ] [ subject ] [ date ]
• More info on this list...