June 2014 Archives by author

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Starting: Sun Jun 1 02:36:04 CEST 2014
Ending: Mon Jun 30 22:47:49 CEST 2014
Messages: 457

• [BioC] ComBat   Rama Akondy
• [BioC] ComBat   Rama Akondy
• [BioC] SRAmetadb Bioconductor package; study record count low for 2013   Al-Nasir, Jamie (2012)
• [BioC] DEXSeqDataSetFromHTSeq Error   Simon Anders
• [BioC] ComBat   Galina Apostolova
• [BioC] makecdfenv package bug   Danny Arends
• [BioC] Renaming the seqlevels in a transcript database from GenomicFeatures   Sonali Arora
• [BioC] ConnectivityMap Package (instances, rankMatrix data)   Azam
• [BioC] edgeR and DESeq2: model design and estimation of dispersion   Iddo Ben-dov
• [BioC] edgeR and DESeq2: model design and estimation of dispersion   Iddo Ben-dov
• [BioC] problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name   Blanchette, Marco
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Caleb Bostwick
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Caleb Bostwick
• [BioC] ComBat --- Got it working for some variables but not others?!   Celine Bourdon
• [BioC] ComBat --- Got it working for some variables but not others?!   Celine Bourdon
• [BioC] epivizr: Input data type for heatmap   Hector Corrada Bravo
• [BioC] Approaches to building Rle sequences from ranges   Vince S. Buffalo
• [BioC] Approaches to building Rle sequences from ranges   Vince S. Buffalo
• [BioC] Approaches to building Rle sequences from ranges   Vince S. Buffalo
• [BioC] Approaches to building Rle sequences from ranges   Vince S. Buffalo
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] GenomicAlignments and QNAME collision   Stefano Calza
• [BioC] readGAlignmentPairsFromBam with yieldSize & which   Stefano Calza
• [BioC] readGAlignmentPairsFromBam with yieldSize & which   Stefano Calza
• [BioC] SNP ID mapping with oligo package (pd.genomewidesnp.6)   Vincent Carey
• [BioC] Transcript clusters missing from hugene20sttranscriptcluster.db   Marc Carlson
• [BioC] annotations for arrays   Marc Carlson
• [BioC] [devteam-bioc] Genomic Features - makeTranscriptDbFromGFF()   Marc Carlson
• [BioC] VariantFiltering: Installation segfault   Robert Castelo
• [BioC] VariantFiltering: Installation segfault   Robert Castelo
• [BioC] GRanges apply functions   Robert Castelo
• [BioC] Renaming the seqlevels in a transcript database from GenomicFeatures   Fong Chun Chan
• [BioC] GenomicAlignments - Speeding up readGAlignmentPairs()   Fong Chun Chan
• [BioC] flowClean   Pratip K. Chattopadhyay
• [BioC] flowClean   Pratip K. Chattopadhyay
• [BioC] Problem with removing duplicated probes of datasets without annotation   Kaj Chokeshaiusaha
• [BioC] Problem with removing duplicated probes of datasets without annotation   Kaj Chokeshaiusaha
• [BioC] GRanges apply functions   Marcin Cieślik
• [BioC] Transcript clusters missing from hugene20sttranscriptcluster.db   Cornwell, Adam
• [BioC] Transcript clusters missing from hugene20sttranscriptcluster.db   Cornwell, Adam
• [BioC] total count filter cutoff (edgeR)   Daniel
• [BioC] create the expression set   Sean Davis
• [BioC] No significant p-values   Sean Davis
• [BioC] External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??   Davis, Wade
• [BioC] Error in Views method c()   Michael Dondrup
• [BioC] error on detecting regions   Pan Du
• [BioC] biomaRt proxy issues   Steffen Durinck
• [BioC] GenomicRanges: removing contained ranges without merging overlapping ranges   Jonathan Ellis
• [BioC] [devteam-bioc] readGappedAlignments not working in Rsamtools   Alvaro F
• [BioC] BioC AMI --instance type   Rohmatul Fajriyah
• [BioC] BioC AMI --instance type   Rohmatul Fajriyah
• [BioC] BioC AMI --instance type   Rohmatul Fajriyah
• [BioC] BioC AMI --instance type   Rohmatul Fajriyah
• [BioC] Deseq for pairwise comparison among many pairs   Feng, Shihai
• [BioC] biomaRt proxy issues   Enrico Ferrero
• [BioC] Flowcore - read.FCS : findOffsets problem??   Greg Finak
• [BioC] error writing empty character string in rhdf5 >= 2.8.0   Bernd Fischer
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] flowClean   Kipper Fletez-Brant
• [BioC] error writing empty character string in rhdf5 >= 2.8.0   Brad Friedman
• [BioC] rhdf5 read/write concurrency surprise   Brad Friedman
• [BioC] crlmm of other software for oncoscan   Richard Friedman
• [BioC] [DIFFBIND] batch effects and blocking factors   Giuseppe Gallone
• [BioC] [DIFFBIND] batch effects and blocking factors   Giuseppe Gallone
• [BioC] Annotation files for bacterial genome RNAseq   Jose Garcia
• [BioC] Limma package and minimal number of genes   Paul Geeleher
• [BioC] Venn diagram with 7 sets   Julian Gehring
• [BioC] epivizr: Input data type for heatmap   Julian Gehring
• [BioC] Query regarding SomatiSignature bioconductor package   Julian Gehring
• [BioC] Query regarding SomatiSignature bioconductor package   Julian Gehring
• [BioC] Query regarding SomatiSignature bioconductor package   Julian Gehring
• [BioC] VariantFiltering: Installation segfault   Julian Gehring
• [BioC] rtracklayer browserView   Dave Gerrard
• [BioC] Limma package and minimal number of genes   Bas van Gestel
• [BioC] Limma package and minimal number of genes   Bas van Gestel
• [BioC] GRanges - coercion from dataframe   Ghost
• [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip   Stephanie M. Gogarten
• [BioC] Custom GeneSetCollection PFAM   Fabian Grammes
• [BioC] GLM in EdgeR   Smith H.
• [BioC] ReportingTools error message   Jason Hackney
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   Jason Hackney
• [BioC] Gviz Incorrect Labels on Features   Hahne, Florian
• [BioC] Warning message while trying to install Bioconductor   Kasper Daniel Hansen
• [BioC] ChIP-Seq Normalization of mutant vs. WT libraries   Kasper Daniel Hansen
• [BioC] Warning message while trying to install Bioconductor   Kasper Daniel Hansen
• [BioC] smoothing function in bumphunter in minfi   Kasper Daniel Hansen
• [BioC] smoothing function in bumphunter in minfi   Kasper Daniel Hansen
• [BioC] smoothing function in bumphunter in minfi   Kasper Daniel Hansen
• [BioC] Behaviour of weights in limma   Paul Harrison
• [BioC] Behaviour of weights in limma   Paul Harrison
• [BioC] readDGE   Chinh Hoan
• [BioC] readDGE   Chinh Hoan
• [BioC] Annotation files for bacterial genome RNAseq   Hans-Rudolf Hotz
• [BioC] Warning message while trying to install Bioconductor   Wolfgang Huber
• [BioC] topGO genes associated with GO terms   Wolfgang Huber
• [BioC] ECCB workshop call for abstracts: "Analysis of Differential Isoform Usage by RNA-seq: Statistical Methodologies and Open Software"   Wolfgang Huber
• [BioC] Problem with removing duplicated probes of datasets without annotation   Wolfgang Huber
• [BioC] VSN with spike-in probes question   Wolfgang Huber
• [BioC] affyxparser -- updating header information   Stacy Hung
• [BioC] Differences between limma voom E values and edgeR cpm values?   John Brothers II
• [BioC] error on detecting regions   Jia, Li (NIH/NCI) [C]
• [BioC] create the expression set   Jia, Li (NIH/NCI) [C]
• [BioC] xy-plot of fcs fails: undefined column selected   Jiang, Mike
• [BioC] ComBat   Johnson, William Evan
• [BioC] Approaches to building Rle sequences from ranges   Johnston, Jeffrey
• [BioC] Thread safety of BSgenome getSeq()   Johnston, Jeffrey
• [BioC] FACS Diva Experiment files import   Pierre-Emmanuel Jouve
• [BioC] dba.counts error   Ravi Karra
• [BioC] dba.counts error   Ravi Karra
• [BioC] biomaRt: getSequence returns "Sequence unavailable" where I'd expect NA   Jan Kim
• [BioC] limma modeling, paired samples   Bernd Klaus
• [BioC] converting probeset id to gene id's : fRMA   Bernd Klaus
• [BioC] wilcox.test error   Axel Klenk
• [BioC] Installing Workflows for Oligonucleotide arrays   Rinaldy Kusuma
• [BioC] DESeq2 new error coming up   Marko Laakso
• [BioC] ComBat() -- run with one sample in one batch   Peter Langfelder
• [BioC] Error when applying ComBat in SCAN.UPC   Peter Langfelder
• [BioC] Error when applying ComBat in SCAN.UPC   Peter Langfelder
• [BioC] Error when applying ComBat in SCAN.UPC   Peter Langfelder
• [BioC] Error installing impute package   Peter Langfelder
• [BioC] ComBat --- Got it working for some variables but not others?!   Peter Langfelder
• [BioC] converting probeset id to gene id's : fRMA   Peter Langfelder
• [BioC] WGCNA_ Eigengene and sample complications correlations   Peter Langfelder
• [BioC] converting probeset id to gene id's : fRMA   Federico Lasa
• [BioC] Annotation files for bacterial genome RNAseq   José Luis Lavín
• [BioC] Annotation files for bacterial genome RNAseq   José Luis Lavín
• [BioC] Annotation files for bacterial genome RNAseq   José Luis Lavín
• [BioC] Annotation files for bacterial genome RNAseq   José Luis Lavín
• [BioC] Annotation files for bacterial genome RNAseq   José Luis Lavín
• [BioC] GRanges - coercion from dataframe   Michael Lawrence
• [BioC] ParseMetaFromGtfFile is.na() error   Michael Lawrence
• [BioC] ParseMetaFromGtfFile is.na() error   Michael Lawrence
• [BioC] GenomicRanges: removing contained ranges without merging overlapping ranges   Michael Lawrence
• [BioC] Approaches to building Rle sequences from ranges   Michael Lawrence
• [BioC] Approaches to building Rle sequences from ranges   Michael Lawrence
• [BioC] Approaches to building Rle sequences from ranges   Michael Lawrence
• [BioC] GenomicRanges select parameter   Michael Lawrence
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Michael Lawrence
• [BioC] GenomicRanges select parameter   Michael Lawrence
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Michael Lawrence
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Michael Lawrence
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Michael Lawrence
• [BioC] Genomic Features - makeTranscriptDbFromGFF()   Michael Lawrence
• [BioC] Creating DataFrame uses too much memory   Michael Lawrence
• [BioC] GRanges apply functions   Michael Lawrence
• [BioC] GRanges apply functions   Michael Lawrence
• [BioC] GRanges apply functions   Michael Lawrence
• [BioC] Types of overlap Iranges   Michael Lawrence
• [BioC] Dates in DataFrames printed incorrectly?   Michael Lawrence
• [BioC] [devteam-bioc] apply function on genomicsRanges ob   Michael Lawrence
• [BioC] Renaming the seqlevels in a transcript database from GenomicFeatures   Michael Lawrence
• [BioC] Can my problem be addressed with Bioconductor?   Leonardi, Michela
• [BioC] GRanges apply functions   Francesco Lescai
• [BioC] GRanges apply functions   Francesco Lescai
• [BioC] DESeqs two-factor two-level, interaction is interested   Shucong Li
• [BioC] GO enrichment analysis for rice genes   Yong Li
• [BioC] Warning message while trying to install Bioconductor   Steve Lianoglou
• [BioC] install previous version of DEXSeq (1.6.0)   Steve Lianoglou
• [BioC] Installation issue with package GenomicRanges_1.17.18.tar.gz   Steve Lianoglou
• [BioC] No significant p-values   Steve Lianoglou
• [BioC] DNAStringSet_translate error in predictCoding()   "Dr. Jörg Linde"
• [BioC] justRMA couldn't obtain CDF environment   Li Liu
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Michael Love
• [BioC] DESeq2 - paired sample, interaction and fold change   Michael Love
• [BioC] DESeq2 - paired sample, interaction and fold change   Michael Love
• [BioC] DESeq2 Error in estimateSizeFactorsForMatrix   Michael Love
• [BioC] Using DESeq2: experimental design and extracting results   Michael Love
• [BioC] DESeq: Hypothesis testing in multifactor design   Michael Love
• [BioC] Using DESeq2: experimental design and extracting results   Michael Love
• [BioC] Using DESeq2: experimental design and extracting results   Michael Love
• [BioC] Deseq for pairwise comparison among many pairs   Michael Love
• [BioC] Using DESeq2: experimental design and extracting results   Michael Love
• [BioC] DESeq2 new error coming up   Michael Love
• [BioC] DESeq2 new error coming up   Michael Love
• [BioC] DESeq analysis of resistance data   Michael Love
• [BioC] edgeR and DESeq2: model design and estimation of dispersion   Michael Love
• [BioC] DESeq analysis of resistance data   Michael Love
• [BioC] DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2   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] No significant p-values   Michael Love
• [BioC] specifying continuous independent variables in DESeq2   Michael Love
• [BioC] specifying continuous independent variables in DESeq2   Michael Love
• [BioC] Error when applying ComBat in SCAN.UPC   Joel Ma
• [BioC] Error when applying ComBat in SCAN.UPC   Joel Ma
• [BioC] Error when applying ComBat in SCAN.UPC   Joel Ma
• [BioC] Error in Data.frame for mogene10stv1cdf and mogene10sttranscriptcluster.db   Joel Ma
• [BioC] makecdfenv package bug   James W. MacDonald
• [BioC] makecdfenv package bug   James W. MacDonald
• [BioC] Transcript clusters missing from hugene20sttranscriptcluster.db   James W. MacDonald
• [BioC] Affymetrix HuGene 2.0 ST annotation   James W. MacDonald
• [BioC] Fwd: limma modeling, paired samples   James W. MacDonald
• [BioC] Error when applying ComBat in SCAN.UPC   James W. MacDonald
• [BioC] limma modeling, paired samples   James W. MacDonald
• [BioC] Error when applying ComBat in SCAN.UPC   James W. MacDonald
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   James W. MacDonald
• [BioC] Installing Workflows for Oligonucleotide arrays   James W. MacDonald
• [BioC] Duplicate probe coordinates with pd.hugene.2.1.st and oligo   James W. MacDonald
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   James W. MacDonald
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   James W. MacDonald
• [BioC] readDGE   James W. MacDonald
• [BioC] readDGE   James W. MacDonald
• [BioC] GenomicFeatures Transcripts Retrieval Fails   James W. MacDonald
• [BioC] GenomicFeatures Transcripts Retrieval Fails   James W. MacDonald
• [BioC] Can my problem be addressed with Bioconductor?   James W. MacDonald
• [BioC] Error in validObject(.Object)   James W. MacDonald
• [BioC] Error in validObject(.Object)   James W. MacDonald
• [BioC] Annotation files for bacterial genome RNAseq   James W. MacDonald
• [BioC] WGCNA_ problem in creating scale free topology plot   James W. MacDonald
• [BioC] Annotation files for bacterial genome RNAseq   James W. MacDonald
• [BioC] Problom in performing Gene Set Test using KEGG   James W. MacDonald
• [BioC] justRMA couldn't obtain CDF environment   James W. MacDonald
• [BioC] create the expression set   James W. MacDonald
• [BioC] merge error: 'by.x' and 'by.y' specify different numbers of columns   James W. MacDonald
• [BioC] how to remove probeset   James W. MacDonald
• [BioC] Error in Data.frame for mogene10stv1cdf and mogene10sttranscriptcluster.db   James W. MacDonald
• [BioC] Using DESeq2: experimental design and extracting results   Sridhar A Malkaram
• [BioC] Using DESeq2: experimental design and extracting results   Sridhar A Malkaram
• [BioC] install previous version of DEXSeq (1.6.0)   Mallon, Eamonn B. (Dr.)
• [BioC] converting probeset id to gene id's : fRMA   Matthew McCall
• [BioC] flowClean   Justin Meskas
• [BioC] flowClean   Justin Meskas
• [BioC] flowClean   Justin Meskas
• [BioC] flowClean   Justin Meskas
• [BioC] flowClean   Justin Meskas
• [BioC] Fwd: limma modeling, paired samples   Riba Michela
• [BioC] limma modeling, paired samples   Riba Michela
• [BioC] limma modeling, paired samples   Riba Michela
• [BioC] question about flowCore dependencies   Mike
• [BioC] Question flowViz   Mike
• [BioC] OpenCyto   Mike
• [BioC] OpenCyto   Mike
• [BioC] Fwd: Guide vers la personne responsable de "read.FCS"?   Mike
• [BioC] Warning message while trying to install Bioconductor   Martin Morgan
• [BioC] Rbowtie - compilation error   Martin Morgan
• [BioC] [devteam-bioc] Worker count specification in functions using bplapply from the BiocParallel pkg   Martin Morgan
• [BioC] Custom GeneSetCollection PFAM   Martin Morgan
• [BioC] BioC2014 travel scholarship deadline June 10   Martin Morgan
• [BioC] readGAlignmentPairsFromBam with yieldSize & which   Martin Morgan
• [BioC] mutant allele read counts   Murli
• [BioC] mutant allele read counts   Murli
• [BioC] mutant allele read counts   Murli
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Sigve Nakken
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] GenomicAlignments and QNAME collision   Valerie Obenchain
• [BioC] VCF class: different length when unlisting INFO CompressedCharacterList   Valerie Obenchain
• [BioC] [devteam-bioc] readGappedAlignments not working in Rsamtools   Valerie Obenchain
• [BioC] mutant allele read counts   Valerie Obenchain
• [BioC] mutant allele read counts   Valerie Obenchain
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Valerie Obenchain
• [BioC] mutant allele read counts   Valerie Obenchain
• [BioC] mutant allele read counts   Valerie Obenchain
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Valerie Obenchain
• [BioC] DNAStringSet_translate error in predictCoding()   Valerie Obenchain
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Valerie Obenchain
• [BioC] DNAStringSet_translate error in predictCoding()   Valerie Obenchain
• [BioC] [devteam-bioc] apply function on genomicsRanges ob   Valerie Obenchain
• [BioC] [devteam-bioc] apply function on genomicsRanges ob   Valerie Obenchain
• [BioC] Creating DataFrame uses too much memory   Ludo Pagie
• [BioC] Error in Views method c()   Hervé Pagès
• [BioC] Thread safety of BSgenome getSeq()   Hervé Pagès
• [BioC] singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big   Hervé Pagès
• [BioC] Elementwise appending of List elements?   Hervé Pagès
• [BioC] singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big   Hervé Pagès
• [BioC] Elementwise appending of List elements?   Hervé Pagès
• [BioC] Renaming the seqlevels in a transcript database from GenomicFeatures   Hervé Pagès
• [BioC] Gviz: Plotting mean & CI for DataTrack   Shraddha Pai
• [BioC] SNP ID mapping with oligo package (pd.genomewidesnp.6)   Solip Park
• [BioC] Gviz Incorrect Labels on Features   Lance Parsons
• [BioC] Creating a package   Matthew Robert Paul
• [BioC] No significant p-values   Lucia Peixoto
• [BioC] No significant p-values   Lucia Peixoto
• [BioC] Opening Data for NormqPCR (readqPCR)   James Perkins
• [BioC] Duplicate probe coordinates with pd.hugene.2.1.st and oligo   Steve Piccolo
• [BioC] FYI: SCAN.UPC and HuGene 1/2 arrays   Steve Piccolo
• [BioC] SCAN.UPC for microarray and RNAseq data   Steve Piccolo
• [BioC] SCAN.UPC for microarray and RNAseq data   Steve Piccolo
• [BioC] SCAN.UPC for microarray and RNAseq data   Steve Piccolo
• [BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?   Lisette de Pillis
• [BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?   Lisette de Pillis
• [BioC] crlmm : copy number and genotyping of Illumina data   Abhishek Pratap
• [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip   Abhishek Pratap
• [BioC] crlmm : copy number and genotyping of Illumina data   Abhishek Pratap
• [BioC] crlmm : copy number and genotyping of Illumina data   Abhishek Pratap
• [BioC] crlmm : copy number and genotyping of Illumina data   Abhishek Pratap
• [BioC] crlmm : copy number and genotyping of Illumina data   Abhishek Pratap
• [BioC] converting probeset id to gene id's : fRMA   Abhishek Pratap
• [BioC] converting probeset id to gene id's : fRMA   Abhishek Pratap
• [BioC] converting probeset id to gene id's : fRMA   Abhishek Pratap
• [BioC] Venn diagram with 7 sets   Alpesh Querer
• [BioC] EasyqPCR package - extracting Standard error values   Tommaso Raffaello
• [BioC] ECCB 2014   Wolfgang Raffelsberger
• [BioC] biomaRt proxy issues   Raynor, Bill
• [BioC] Rbowtie - compilation error   Romain Retureau
• [BioC] question about how to understand exon usage coefficient value   Alejandro Reyes
• [BioC] non specific filtering 27k methlylation chip   Martin Rijlaarsdam
• [BioC] crlmm : copy number and genotyping of Illumina data   Matt Ritchie
• [BioC] crlmm : copy number and genotyping of Illumina data   Matt Ritchie
• [BioC] Contrast among a subset of interactions, glm in edgeR   Maximo Rivarola
• [BioC] Contrast among a subset of interactions, glm in edgeR   Maximo Rivarola
• [BioC] Contrast among a subset of interactions, glm in edgeR   Maximo Rivarola
• [BioC] Contrast among a subset of interactions, glm in edgeR   Maximo Rivarola
• [BioC] Contrast among a subset of interactions, glm in edgeR   Maximo Rivarola
• [BioC] Possible problem with featureCounts() and scipen   Oscar Rueda
• [BioC] Practical Workshop on High-Throughput Sequencing Data Analysis. 6-10 Oct 2014, OIST, Okinawa, Japan   Gabriella Rustici
• [BioC] smoothing function in bumphunter in minfi   Ruzicka, William B.,M.D.
• [BioC] GRanges - coercion from dataframe   Ryan
• [BioC] Limma package and minimal number of genes   Ryan
• [BioC] Limma package and minimal number of genes   Ryan
• [BioC] edgeR and DESeq2: model design and estimation of dispersion   Ryan
• [BioC] Contrast among a subset of interactions, glm in edgeR   Ryan
• [BioC] EB Seq conditions   Sabet, Julia A
• [BioC] Error when applying ComBat in SCAN.UPC   Natasha Sahgal
• [BioC] Installation issue with package GenomicRanges_1.17.18.tar.gz   Minita Shah
• [BioC] SRAmetadb Bioconductor package; study record count low for 2013   Hugh Shanahan
• [BioC] ConnectivityMap Package (instances, rankMatrix data)   Paul Shannon
• [BioC] Possible problem with featureCounts() and scipen   Wei Shi
• [BioC] Incorrect result in edgeR.calculateCommonDispersion   Jacob Silterra
• [BioC] Incorrect result in edgeR.calculateCommonDispersion   Jacob Silterra
• [BioC] p-values from robust linear model in LIMMA   Gordon K Smyth
• [BioC] Differences between limma voom E values and edgeR cpm values?   Gordon K Smyth
• [BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?   Gordon K Smyth
• [BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?   Gordon K Smyth
• [BioC] Behaviour of weights in limma   Gordon K Smyth
• [BioC] Incorrect result in edgeR.calculateCommonDispersion   Gordon K Smyth
• [BioC] Incorrect result in edgeR.calculateCommonDispersion   Gordon K Smyth
• [BioC] p-values from robust linear model in LIMMA   Gordon K Smyth
• [BioC] edgeR and DESeq2: model design and estimation of dispersion   Gordon K Smyth
• [BioC] GLM in EdgeR   Gordon K Smyth
• [BioC] cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]   Gordon K Smyth
• [BioC] Contrast among a subset of interactions, glm in edgeR   Gordon K Smyth
• [BioC] Contrast among a subset of interactions, glm in edgeR   Gordon K Smyth
• [BioC] [DIFFBIND] batch effects and blocking factors   Gordon K Smyth
• [BioC] p-values from robust linear model in LIMMA   Arvid Sondén
• [BioC] p-values from robust linear model in LIMMA   Arvid Sondén
• [BioC] wilcox.test error   Nikul Soni
• [BioC] limma lmFit warnings   Nikul Soni
• [BioC] Rbowtie - compilation error   Michael Stadler
• [BioC] Rbowtie - compilation error   Michael Stadler
• [BioC] Rbowtie - compilation error   Michael Stadler
• [BioC] Rbowtie - compilation error   Michael Stadler
• [BioC] Could you help us about DiffBind   Rory Stark
• [BioC] dba.counts error   Rory Stark
• [BioC] DiffBind, dba.count result object   Rory Stark
• [BioC] Subject: Re: [DIFFBIND] batch effects and blocking factors   Rory Stark
• [BioC] loessByCluster returning error in smooth function in bumphunter   Jiayi Sun
• [BioC] loessByCluster returning error in smooth function in bumphunter   Jiayi Sun
• [BioC] Error in validObject(.Object)   Surles, Monique
• [BioC] Error in validObject(.Object)   Surles, Monique
• [BioC] BioC AMI --instance type   Dan Tenenbaum
• [BioC] Installing Workflows for Oligonucleotide arrays   Dan Tenenbaum
• [BioC] [devteam-bioc] error: 'BiocInstaller' package not in repository   Dan Tenenbaum
• [BioC] error: 'BiocInstaller' package not in repository   Dan Tenenbaum
• [BioC] Error installing impute package   Dan Tenenbaum
• [BioC] Error installing impute package   Dan Tenenbaum
• [BioC] rtracklayer browserView   Dan Tenenbaum
• [BioC] loading qvalue library causes R to abort   Dan Tenenbaum
• [BioC] Elementwise appending of List elements?   Ryan C. Thompson
• [BioC] Elementwise appending of List elements?   Ryan C. Thompson
• [BioC] Dates in DataFrames printed incorrectly?   Ryan C. Thompson
• [BioC] VSN with spike-in probes question   Thornton, Matthew
• [BioC] External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??   Thornton, Matthew
• [BioC] External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??   Thornton, Matthew
• [BioC] GRanges apply functions   Tim Triche, Jr.
• [BioC] GRanges apply functions   Tim Triche, Jr.
• [BioC] xy-plot of fcs fails: undefined column selected   Tobias Timmel
• [BioC] merge error: 'by.x' and 'by.y' specify different numbers of columns   Tran, Nhu Quynh T
• [BioC] ChIP-Seq Normalization of mutant vs. WT libraries   Minerva Trejo
• [BioC] GenomicRanges select parameter   Karolis Uziela
• [BioC] GenomicRanges select parameter   Karolis Uziela
• [BioC] GenomicRanges select parameter   Karolis Uziela
• [BioC] Error installing impute package   Levi Waldron
• [BioC] biomaRt timeout solution?   Xiaokuan Wei
• [BioC] GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)   Luo Weijun
• [BioC] GAGE RNA-Seq analysis for for a fungi species cryptococcus_neoformans   Luo Weijun
• [BioC] DESeq analysis of resistance data   Dave Wettmann
• [BioC] No significant p-values   Dave Wettmann
• [BioC] No significant p-values   Dave Wettmann
• [BioC] ParseMetaFromGtfFile is.na() error   Beth Wilmot
• [BioC] ReportingTools error message   Assa Yeroslaviz
• [BioC] ReportingTools error message   Assa Yeroslaviz
• [BioC] GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?   Janet Young
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Janet Young
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Janet Young
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Janet Young
• [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?   Janet Young
• [BioC] specifying continuous independent variables in DESeq2   Jorge Zamora
• [BioC] specifying continuous independent variables in DESeq2   Jorge Zamora
• [BioC] segfault in rqubic   Zhang, Jitao David
• [BioC] SRAmetadb Bioconductor package; study record count low for 2013   Jack Zhu
• [BioC] SRAmetadb Bioconductor package; study record count low for 2013   Jack Zhu
• [BioC] DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2   Aditi [guest]
• [BioC] Problom in performing Gene Set Test using KEGG   Aditya [guest]
• [BioC] topGO genes associated with GO terms   Agnieszka Golicz [guest]
• [BioC] readGappedAlignments not working in Rsamtools   Alvaro [guest]
• [BioC] Query regarding SomatiSignature bioconductor package   Anand [guest]
• [BioC] DEXSeqDataSetFromHTSeq Error   Attila [guest]
• [BioC] ParseMetaFromGtfFile is.na() error   Beth Wilmot [guest]
• [BioC] error in subsetting GeneFeatureSet with Oligo   Bruno [guest]
• [BioC] Opening Data for NormqPCR (readqPCR)   Camille [guest]
• [BioC] DESeq analysis of resistance data   Dave Wettmann [guest]
• [BioC] No significant p-values   Dave Wettmann [guest]
• [BioC] Genomic Features - makeTranscriptDbFromGFF()   Geoffrey Thomson [guest]
• [BioC] apply function on genomicsRanges ob   Greg VOISIN [guest]
• [BioC] ComBat() -- run with one sample in one batch   Guest [guest]
• [BioC] install previous version of DEXSeq (1.6.0)   Hatice [guest]
• [BioC] Worker count specification in functions using bplapply from the BiocParallel pkg   Jerry Davison [guest]
• [BioC] Problem with removing duplicated probes of datasets without annotation   Kaj Chokeshaiusaha [guest]
• [BioC] loading qvalue library causes R to abort   Kim S [guest]
• [BioC] PostDoc opportunity   Marc Hild [guest]
• [BioC] Can my problem be addressed with Bioconductor?   Michela Leonardi [guest]
• [BioC] virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'   Mick Elliot [guest]
• [BioC] annotations for arrays   Miki Blumenberg [guest]
• [BioC] mutant allele read counts   Murli [guest]
• [BioC] Affymetrix HuGene 2.0 ST annotation   Natasha [guest]
• [BioC] non specific filtering 27k methlylation chip   Ninni Nahm [guest]
• [BioC] how to remove probeset   Quan [guest]
• [BioC] Installing Workflows for Oligonucleotide arrays   Rinaldy K [guest]
• [BioC] Rbowtie - compilation error   Romain [guest]
• [BioC] compiler error: Rbowtie   Romz34 [guest]
• [BioC] HTqPCR package data layout - how flexible is it?   Ruben Alvarez [guest]
• [BioC] SNP ID mapping with Oligo package   Solip [guest]
• [BioC] Complex between and within sample design   Tobias Neumann [guest]
• [BioC] xy-plot of fcs fails: undefined column selected   Tobias Timmel [guest]
• [BioC] error: 'BiocInstaller' package not in repository   Vrakj [guest]
• [BioC] error: 'BiocInstaller' package not in repository   Vrakj [guest]
• [BioC] error on detecting regions   guest [guest]
• [BioC] create the expression set   guest [guest]
• [BioC] DESeq: Hypothesis testing in multifactor design   yanzhu [guest]
• [BioC] DESeq2 - paired sample, interaction and fold change   samuel collombet
• [BioC] DESeq2 - paired sample, interaction and fold change   samuel collombet
• [BioC] External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??   cstrato
• [BioC] justRMA couldn't obtain CDF environment   cstrato
• [BioC] Opening Data for NormqPCR (readqPCR)   camille daugrois
• [BioC] GenomicFeatures Transcripts Retrieval Fails   sharvari gujja
• [BioC] Flowcore - read.FCS : findOffsets problem??   Gaël kaneko
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Sharvari.Gujja at sanofi.com
• [BioC] WGCNA_ problem in creating scale free topology plot   amit kumar subudhi
• [BioC] WGCNA_ Eigengene and sample complications correlations   amit kumar subudhi
• [BioC] apply function on genomicsRanges obj   gregory voisin
• [BioC] [devteam-bioc] apply function on genomicsRanges ob   gregory voisin
• [BioC] SCAN.UPC for microarray and RNAseq data   shirley zhang
• [BioC] SCAN.UPC for microarray and RNAseq data   shirley zhang
• [BioC] SCAN.UPC for microarray and RNAseq data   shirley zhang
• [BioC] SCAN.UPC for microarray and RNAseq data   shirley zhang
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   张超
• [BioC] Issues about how to use rma and paCalls to filter probe sets together   张超
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   张超
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   张超
• [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets   张超
• [BioC] Could you help us about DiffBind   賴勇志
• [BioC] Could you help us about DiffBind   賴勇志

Last message date: Mon Jun 30 22:47:49 CEST 2014
Archived on: Tue Jul 1 18:46:21 CEST 2014

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