July 2012 Archives by author

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Starting: Sun Jul 1 02:45:34 CEST 2012
Ending: Tue Jul 31 21:48:17 CEST 2012
Messages: 631

• [BioC] edgeR, glmLRT error   Cei Abreu-Goodger
• [BioC] edgeR, glmLRT error   Cei Abreu-Goodger
• [BioC] edgeR, glmLRT error   Cei Abreu-Goodger
• [BioC] Linkage Disequilibrium Analysis   Ovokeraye Achinike-Oduaran
• [BioC] Linkage Disequilibrium Analysis   Ovokeraye Achinike-Oduaran
• [BioC] Linkage Disequilibrium Analysis   Ovokeraye Achinike-Oduaran
• [BioC] BiomaRt - Flanking regions   Ovokeraye Achinike-Oduaran
• [BioC] BiomaRt - Flanking regions   Ovokeraye Achinike-Oduaran
• [BioC] overview function of made4   Aedin
• [BioC] Problems with iteration (sappily) over RNAStringSet   Kemal Akat
• [BioC] easyRNAseq question   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] counts from HTSeq vs DEXSeq   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] counts from HTSeq vs DEXSeq   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] error in DEXSeq version 1.3.13   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] clarification on DEXSeq output   Akula, Nirmala (NIH/NIMH) [C]
• [BioC] Fwd: edgeR dispersions   Guffanti Alessandro
• [BioC] Fwd: edgeR dispersions   Guffanti Alessandro
• [BioC] how to count for edgeR input   Guffanti Alessandro
• [BioC] how to count for edgeR input   Guffanti Alessandro
• [BioC] limma voom: How to create double contrasts?   Christian Ametz
• [BioC] Antw: Re: limma voom: How to create double contrasts?   Christian Ametz
• [BioC] Antw: Re: limma voom: How to create double contrasts?   Christian Ametz
• [BioC] Antw: Re: limma voom: How to create double contrasts?   Christian Ametz
• [BioC] multicore and DEXSeq   Lynn Amon
• [BioC] multicore and DEXSeq   Lynn Amon
• [BioC] multicore and DEXSeq   Lynn Amon
• [BioC] multicore and DEXSeq   Lynn Amon
• [BioC] Reproducibility in DESeq   Simon Anders
• [BioC] counts from HTSeq vs DEXSeq   Simon Anders
• [BioC] Why org.At.tair.db is named differently?   Simon Anders
• [BioC] clarification on DEXSeq output   Simon Anders
• [BioC] EBImage Sample code errors   Robert Baer
• [BioC] EBImage Sample code errors   Robert Baer
• [BioC] EBImage Sample code errors   Robert Baer
• [BioC] Another question about normalization of data   Gustavo Fernández Bayón
• [BioC] Another question about normalization of data   Gustavo Fernández Bayón
• [BioC] Clustering question   Gustavo Fernández Bayón
• [BioC] Clustering question   Gustavo Fernández Bayón
• [BioC] Simple conceptual question   Gustavo Fernández Bayón
• [BioC] Simple conceptual question   Gustavo Fernández Bayón
• [BioC] Testing for no difference   Gustavo Fernández Bayón
• [BioC] Testing for no difference   Gustavo Fernández Bayón
• [BioC] Testing for no difference   Gustavo Fernández Bayón
• [BioC] Testing for no difference   Gustavo Fernández Bayón
• [BioC] Testing for no difference   Gustavo Fernández Bayón
• [BioC] EasyRNASeq issue (missing bai files)   Jorge Beira
• [BioC] R 2.15.1 ReadAffy error   Henrik Bengtsson
• [BioC] R 2.15.1 ReadAffy error   Ben Bolstad
• [BioC] DiffBind error loading dba.count   Gordon Brown
• [BioC] IRanges problem: findOverlaps   Jonathan Cairns
• [BioC] College bioinformatics project suggestions?   Caitlin
• [BioC] Linkage Disequilibrium Analysis   Vincent Carey
• [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies   Vincent Carey
• [BioC] ReadVcf Memory Issues   Vincent Carey
• [BioC] Calculate heterozygosity % using SNP genotype data   Vincent Carey
• [BioC] Calculate heterozygosity % using SNP genotype data   Vincent Carey
• [BioC] Calculate heterozygosity % using SNP genotype data   Vincent Carey
• [BioC] reading fasta file into R   Vincent Carey
• [BioC] AnnotationDbi: NewSchema vignette error   Marc Carlson
• [BioC] AffyID mapping question   Marc Carlson
• [BioC] pathway ID in KEGG.db   Marc Carlson
• [BioC] Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays   Marc Carlson
• [BioC] pathway ID in KEGG.db   Marc Carlson
• [BioC] illuminaHumanv4.db missing keys in last version   Marc Carlson
• [BioC] How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?   Marc Carlson
• [BioC] entrez gene summary   Marc Carlson
• [BioC] lumi - limma - geneSymbol/geneName   Marc Carlson
• [BioC] Oligo package, possible bug in paCalls   Benilton Carvalho
• [BioC] Oligo package, possible bug in paCalls   Benilton Carvalho
• [BioC] regenerate CEL file from analyzed data   Benilton Carvalho
• [BioC] help with genotyping   Benilton Carvalho
• [BioC] help with genotyping   Benilton Carvalho
• [BioC] Influence of expression correlation on false positive ratio   Robert Castelo
• [BioC] DEXSeq error   Chuming Chen
• [BioC] DEXSeq error   Chuming Chen
• [BioC] DEXSeq error   Chuming Chen
• [BioC] access Limma objects   Chuming Chen
• [BioC] GO enrichment significance   Yao Chen
• [BioC] #Identify differentially expressed genes   Yao Chen
• [BioC] #Identify differentially expressed genes   Yao Chen
• [BioC] Affy mas5 scaling   Yao Chen
• [BioC] [LIMMA]lmFit with continuous predictor   Yao Chen
• [BioC] Testing for no difference   Yao Chen
• [BioC] Linkage Disequilibrium Analysis   Mete Civelek
• [BioC] AffyID mapping question   Kevin Coombes
• [BioC] one-sided (was: expression status from pvalues)   Kevin R. Coombes
• [BioC] Influence of expression correlation on false positive ratio   Kevin R. Coombes
• [BioC] one-sided   Kevin R. Coombes
• [BioC] Normalization of array leads to decrease in number of differentially expressed genes   Kevin R. Coombes
• [BioC] problems reading fcs files / flowcore / read.fcs   David Corne
• [BioC] AnnotationDbi: NewSchema vignette error   Mark Cowley
• [BioC] Limma: how to obtain P values using method "global" for multiple testing   Mark Cruickshank
• [BioC] Normalization of array leads to decrease in number of differentially expressed genes   Cytochalasin
• [BioC] Help with choice of normalization   Cytochalasin
• [BioC] IRanges problem: findOverlaps   Nicolas DESCOSTES
• [BioC] IRanges problem: findOverlaps   Nicolas DESCOSTES
• [BioC] How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?   Philippe DESSEN
• [BioC] Counting reads for edgeR or voom()   Cittaro Davide
• [BioC] Error using impute.knn function   Peter Davidsen
• [BioC] goTools: Error in goidvect[test] : invalid subscript type \'list\'   Brad Davis
• [BioC] correlation coefficient for microarray biological replicates   Sean Davis
• [BioC] Agilent arrays 2- or 1-color?   Sean Davis
• [BioC] Agilent arrays 2- or 1-color?   Sean Davis
• [BioC] Agilent arrays 2- or 1-color?   Sean Davis
• [BioC] report a problem of DESeq   Marcus Davy
• [BioC] reading fasta file into R   Marcus Davy
• [BioC] Getting the length of every element from a large CompressedIRangesList is slow   Nicolas Delhomme
• [BioC] Getting the length of every element from a large CompressedIRangesList is slow   Nicolas Delhomme
• [BioC] Getting the length of every element from a large CompressedIRangesList is slow   Nicolas Delhomme
• [BioC] IRanges: the width argument of the coverage function   Nicolas Delhomme
• [BioC] IRanges coverage integer limit?   Nicolas Delhomme
• [BioC] IRanges coverage integer limit?   Nicolas Delhomme
• [BioC] reads of different lengths (easyRNASeq)   Nicolas Delhomme
• [BioC] IRanges problem: findOverlaps   Nicolas Delhomme
• [BioC] IRanges coverage integer limit?   Nicolas Delhomme
• [BioC] IRanges coverage integer limit?   Nicolas Delhomme
• [BioC] EasyRNASeq issue (missing bai files)   Nicolas Delhomme
• [BioC] EasyRNASeq issue (missing bai files)   Nicolas Delhomme
• [BioC] EasyRNASeq issue (missing bai files)   Nicolas Delhomme
• [BioC] EasyRNASeq issue (missing bai files)   Nicolas Delhomme
• [BioC] EasyRNASeq issue (missing bai files)   Nicolas Delhomme
• [BioC] Warnings with running easyRNASeq with easyRNASeq tutorial   Nicolas Delhomme
• [BioC] Why does a call to "unique" removes a DNAStringSet names?   Nicolas Delhomme
• [BioC] Row labels in a heatmap   Dan Du
• [BioC] undocumented behavior in tilingArray::costMatrix [Scanned]   Du, Yang
• [BioC] Installation Trouble for bioc packages (FunciSNP, RSNPper) for v 2.15.1 (64-pc-linux-gnu (64-bit))   Timothy Duff
• [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies   Timothy Duff
• [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies   Timothy Duff
• [BioC] ReadVcf Memory Issues   Timothy Duff
• [BioC] HTqPCR problems   Heidi Dvinge
• [BioC] miRNA exiqon panels and HTqPCR   Heidi Dvinge
• [BioC] HTqPCR plotting groups of interest   Heidi Dvinge
• [BioC] HTqPCR plotting groups of interest   Heidi Dvinge
• [BioC] HTqPCR problems   Heidi Dvinge
• [BioC] HTqPCR problems   Heidi Dvinge
• [BioC] pathway ID in KEGG.db   Ed
• [BioC] pathway ID in KEGG.db   Ed
• [BioC] comparing qpcr and chip   Marco Fabbri
• [BioC] Survival analysis (hazard ratio calculation)   Farscape2012
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Finak, Greg
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Finak, Greg
• [BioC] flowQ loading issue   Finak, Greg
• [BioC] flowQ loading issue   Fletez-Brant, Christopher (NIH/VRC) [C]
• [BioC] flowQ loading issue   Fletez-Brant, Christopher (NIH/VRC) [C]
• [BioC] Error message running through CQN Vignette   Richard Friedman
• [BioC] Warnings with running easyRNASeq with easyRNASeq tutorial   Richard Friedman
• [BioC] IRanges problem: findOverlaps   Julien Gagneur
• [BioC] Exporting in XPS   Lavorgna Giovanni
• [BioC] Linkage Disequilibrium Analysis   Stephanie M. Gogarten
• [BioC] Translating AB/BB/AA into a SNP with Illumina data   Stephanie M. Gogarten
• [BioC] Translating AB/BB/AA into a SNP with Illumina data   Stephanie M. Gogarten
• [BioC] Translating AB/BB/AA into a SNP with Illumina data   Lavinia Gordon
• [BioC] Translating AB/BB/AA into a SNP with Illumina data   Lavinia Gordon
• [BioC] regenerate CEL file from analyzed data   J. Greenbaum
• [BioC] regenerate CEL file from analyzed data   J. Greenbaum
• [BioC] IRanges problem: findOverlaps   Ivan Gregoretti
• [BioC] help needed - 7 array time course gene expression no replicates - fold change calculation   Liat Shavit Grievink
• [BioC] Row labels in a heatmap   Liat Shavit Grievink
• [BioC] Row labels in a heatmap   Liat Shavit Grievink
• [BioC] Rsamtools: Read a bam line by line   Alex Gutteridge
• [BioC] missing figure text in arrayQualityMetrics   Daniel Aaen Hansen
• [BioC] R 2.15.1 ReadAffy error   Kasper Daniel Hansen
• [BioC] R 2.15.1 ReadAffy error   Kasper Daniel Hansen
• [BioC] R 2.15.1 ReadAffy error   Kasper Daniel Hansen
• [BioC] R 2.15.1 ReadAffy error   Kasper Daniel Hansen
• [BioC] Counting reads for edgeR or voom()   Kasper Daniel Hansen
• [BioC] Error message running through CQN Vignette   Kasper Daniel Hansen
• [BioC] Another question about normalization of data   Kasper Daniel Hansen
• [BioC] Selecting elements in GRanges object by element metadata   Kasper Daniel Hansen
• [BioC] regenerate CEL file from analyzed data   Kasper Daniel Hansen
• [BioC] CQN normalization   Kasper Daniel Hansen
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   Yuan Hao
• [BioC] Using readBAM function in segmentSeq   Tom Hardcastle
• [BioC] Registration is now open for COMBINE 2012. Aug.15-19 in Toronto, Canada   Robin Haw
• [BioC] affylmGUI/biocReposList() Problem   Burkhard Heil
• [BioC] affylmGUI/biocReposList() Problem   Burkhard Heil
• [BioC] affylmGUI/biocReposList() Problem   Burkhard Heil
• [BioC] down-expression and high-expression in single cell + amplification   Dror Hibsh
• [BioC] Can the normalization factors be too far apart in EdgeR analyses?   Hoskins, Jason (NIH/NCI) [F]
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   Jinyan Huang
• [BioC] missing figure text in arrayQualityMetrics   Wolfgang Huber
• [BioC] Help on invariantset normalization function   Wolfgang Huber
• [BioC] DESeq analysis   Wolfgang Huber
• [BioC] easyRNAseq question   Wolfgang Huber
• [BioC] DEseq and FDR correction   Wolfgang Huber
• [BioC] easyRNAseq question   Wolfgang Huber
• [BioC] EBImage installation problem on Linux   Wolfgang Huber
• [BioC] Influence of expression correlation on false positive ratio   Wolfgang Huber
• [BioC] DEXSeq error   Wolfgang Huber
• [BioC] Influence of expression correlation on false positive ratio   Wolfgang Huber
• [BioC] Question regarding cellhts2 output   Wolfgang Huber
• [BioC] correlation coefficient for microarray biological replicates   Wolfgang Huber
• [BioC] Testing for no difference   Wolfgang Huber
• [BioC] Testing for no difference   Wolfgang Huber
• [BioC] a possible bug in DESeq   Wolfgang Huber
• [BioC] a possible bug in DESeq   Wolfgang Huber
• [BioC] help with genotyping   Pina Iannelli
• [BioC] help with genotyping   Pina Iannelli
• [BioC] Converting floating point RangedData to Rle   Marcin Imielinski
• [BioC] two channel data normalization limma   Maite Iriondo
• [BioC] limma time course analysis userguide example for two color microarray   Maite Iriondo
• [BioC] Problem with R453Plus1 Toolbox and files from a Roche GS Junior   Olivia Jardin-Mathé
• [BioC] edge R- p-value   chris Jhon
• [BioC] minor allele frequency comparison from two softwares based on the same sequencing data   Jiafen
• [BioC] edgeR- data for case studies   Johnson, Franklin Theodore
• [BioC] Install details for root level administrators   Paul Johnson
• [BioC] Testing for no difference   Albyn Jones
• [BioC] nem package, nem.BN learning with 'continuous_Baysian' not possible   Siebourg Juliane
• [BioC] entrez gene summary   Amit Kumar Kashyap
• [BioC] Job offer: Computational Biologist, Oncology Novartis   Kauffmann, Audrey
• [BioC] affylmGUI/biocReposList() Problem   Keith
• [BioC] Is it recommended to remove control probes for Agilent type data   Ketaki
• [BioC] illuminaHumanv4.db missing keys in last version   Amos Kirilovsky
• [BioC] FARMS package (fwd)   Günter Klambauer
• [BioC] BIoconductor AMI with R version 2.15.1   Jeff Knisley
• [BioC] #Identify differentially expressed genes   Paolo Kunderfranco
• [BioC] lumi - construct a design matrix   Paolo Kunderfranco
• [BioC] ChIPpeakAnno - Annotation of miRNA   Paolo Kunderfranco
• [BioC] ChIPpeakAnno to find peaks nearest to miRNA   Paolo Kunderfranco
• [BioC] ChIPpeakAnno to find peaks nearest to miRNA   Paolo Kunderfranco
• [BioC] DiffBind error loading dba.count   Paolo Kunderfranco
• [BioC] lumi - limma - geneSymbol/geneName   Paolo Kunderfranco
• [BioC] SWAN normalization for HumanMethylation450K - minfi   Lucia Lam
• [BioC] SWAN normalization for HumanMethylation450K - minfi   Lucia Lam
• [BioC] Help on invariantset normalization function   Sophie Lamarre
• [BioC] Help on invariantset normalization function   Sophie Lamarre
• [BioC] Help on invariantset normalization function   Sophie Lamarre
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   Michael Lawrence
• [BioC] Problems with ggbio   Michael Lawrence
• [BioC] GappedAlignmentPairs requests   Michael Lawrence
• [BioC] GappedAlignmentPairs requests   Michael Lawrence
• [BioC] GappedAlignmentPairs requests   Michael Lawrence
• [BioC] Selecting elements in GRanges object by element metadata   Michael Lawrence
• [BioC] IRanges problem: findOverlaps   Michael Lawrence
• [BioC] Wig files?   Michael Lawrence
• [BioC] rtracklayer import.gff3 mangling scores   Michael Lawrence
• [BioC] Coverage of reads per base position from BAM files   Michael Lawrence
• [BioC] Surrogate variable analysis fails with “subscript out of bounds”   Jeff Leek
• [BioC] Influence of expression correlation on false positive ratio   Jeff Leek
• [BioC] Basic question about analysis of unbalanced design in microarray experiment   Guido Leoni
• [BioC] general question about omogeneity of variances between microarray groups   Guido Leoni
• [BioC] exomeCopy - no .Internal function 'cov' error   Lescai, Francesco
• [BioC] exomeCopy - no .Internal function 'cov' error   Lescai, Francesco
• [BioC] Is it recommended to remove control probes for Agilent type data   Yong Li
• [BioC] AffyID mapping question   Steve Lianoglou
• [BioC] AffyID mapping question   Steve Lianoglou
• [BioC] report a problem of DESeq   Steve Lianoglou
• [BioC] How can I obtain gene name from chromosome location?   Steve Lianoglou
• [BioC] how to count for edgeR input   Steve Lianoglou
• [BioC] edgeR: design matrix for different condition   KJ Lim
• [BioC] edgeR: design matrix for different condition   KJ Lim
• [BioC] edgeR: design matrix for different condition   KJ Lim
• [BioC] edgeR: design matrix for different condition   KJ Lim
• [BioC] Error fom XPS installation   Liu, Binbin
• [BioC] Surrogate variable analysis fails with “subscript out of bounds”   Vebjorn Ljosa
• [BioC] Surrogate variable analysis fails with “subscript out of bounds”   Vebjorn Ljosa
• [BioC] question regarding using cummeRbund package   Jack Luo
• [BioC] question regarding using cummeRbund package   Jack Luo
• [BioC] question regarding using cummeRbund package   Jack Luo
• [BioC] Help on invariantset normalization function   James W. MacDonald
• [BioC] Help on invariantset normalization function   James W. MacDonald
• [BioC] Re : Filtering of data   James W. MacDonald
• [BioC] Re : Filtering of data   James W. MacDonald
• [BioC] Help with GSEAlm   James W. MacDonald
• [BioC] affylmGUI/biocReposList() Problem   James W. MacDonald
• [BioC] affylmGUI/biocReposList() Problem   James W. MacDonald
• [BioC] affylmGUI/biocReposList() Problem   James W. MacDonald
• [BioC] goTools: Error in goidvect[test] : invalid subscript type \'list\'   James W. MacDonald
• [BioC] Limma topTable; fold changes look completely different to the normalized data and Limma fold change   James W. MacDonald
• [BioC] Limma topTable; fold changes look completely different to the normalized data and Limma fold change   James W. MacDonald
• [BioC] Survival analysis (hazard ratio calculation)   James W. MacDonald
• [BioC] help needed - 7 array time course gene expression no replicates - fold change calculation   James W. MacDonald
• [BioC] expression status from pvalues   James W. MacDonald
• [BioC] what is the default parameters of estimateDispersions in the DESeq   James W. MacDonald
• [BioC] College bioinformatics project suggestions?   James W. MacDonald
• [BioC] Row labels in a heatmap   James W. MacDonald
• [BioC] access Limma objects   James W. MacDonald
• [BioC] Row labels in a heatmap   James W. MacDonald
• [BioC] BiomaRt - Flanking regions   James W. MacDonald
• [BioC] BiomaRt - Flanking regions   James W. MacDonald
• [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?   James W. MacDonald
• [BioC] limma voom: How to create double contrasts?   James W. MacDonald
• [BioC] Antw: Re: limma voom: How to create double contrasts?   James W. MacDonald
• [BioC] Antw: Re: limma voom: How to create double contrasts?   James W. MacDonald
• [BioC] how to design comparision using edgeR   James W. MacDonald
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   James W. MacDonald
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   James W. MacDonald
• [BioC] boxplot a big list?   James W. MacDonald
• [BioC] [EDGER] Normalization issue   James W. MacDonald
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   James W. MacDonald
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   James W. MacDonald
• [BioC] edgeR: generating a correct design matrix - multifactorial design   James W. MacDonald
• [BioC] edgeR: generating a correct design matrix - multifactorial design   James W. MacDonald
• [BioC] LIMMA -- obtaining values used to calculate lfc   James W. MacDonald
• [BioC] Installation of XCMS / mzR failed   James W. MacDonald
• [BioC] general question about omogeneity of variances between microarray groups   James W. MacDonald
• [BioC] expression status from pvalues   Alyaa Mahmoud
• [BioC] expression status from pvalues   Alyaa Mahmoud
• [BioC] one-sided (was: expression status from pvalues)   Alyaa Mahmoud
• [BioC] Re : Filtering of data   Deeksha Malhan
• [BioC] DiffBind error with DBA_DESEQ_GLM and warning with DBA_EDGE_GLM   Elisabetta Manduchi
• [BioC] GO enrichment significance   Grimes Mark
• [BioC] GO enrichment significance   Grimes Mark
• [BioC] GO enrichment significance   Grimes Mark
• [BioC] draw path-diagram Rgraphvis   René Mayer
• [BioC] HTqPCR plotting groups of interest   Simon Melov
• [BioC] HTqPCR plotting groups of interest   Simon Melov
• [BioC] HTqPCR problems   Simon Melov
• [BioC] HTqPCR problems   Simon Melov
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Mike
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Mike
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Mike
• [BioC] Coordinate Question for Rgraphviz   Martin Morgan
• [BioC] overview function of made4   Martin Morgan
• [BioC] Rsamtools::countBam returning in correct counts   Martin Morgan
• [BioC] ShortRead package   Martin Morgan
• [BioC] Rsamtools: Read a bam line by line   Martin Morgan
• [BioC] Rsamtools installation error   Martin Morgan
• [BioC] Rsamtools installation error   Martin Morgan
• [BioC] Rsamtools installation error   Martin Morgan
• [BioC] Reading Paired End Native Report Format in ShortRead   Martin Morgan
• [BioC] edgeR and tagwise dispersion: overcorrection for multiple tests?   Martin Morgan
• [BioC] Bioc 2012 Schedule   Martin Morgan
• [BioC] exomeCopy - no .Internal function 'cov' error   Martin Morgan
• [BioC] Reading Paired End Native Report Format in ShortRead   Martin Morgan
• [BioC] [devteam-bioc] Coverage of reads per base position from BAM files   Martin Morgan
• [BioC] Install details for root level administrators   Martin Morgan
• [BioC] ReadVcf Memory Issues   Martin Morgan
• [BioC] Coverage of reads per base position from BAM files   Mukherjee, Rithun
• [BioC] Problems with ggbio   Michael Muratet
• [BioC] Selecting elements in GRanges object by element metadata   Michael Muratet
• [BioC] Selecting elements in GRanges object by element metadata   Michael Muratet
• [BioC] Rsamtools installation error   Murli
• [BioC] Rsamtools installation error   Murli
• [BioC] Rsamtools installation error   Murli
• [BioC] Reading Paired End Native Report Format in ShortRead   Murli
• [BioC] Reading Paired End Native Report Format in ShortRead   Murli
• [BioC] Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays   Karthik K N
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Karthik K N
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Karthik K N
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Karthik K N
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Kieran O'Neill
• [BioC] question regarding using cummeRbund package   Valerie Obenchain
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   Valerie Obenchain
• [BioC] Linkage Disequilibrium Analysis   Valerie Obenchain
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   Valerie Obenchain
• [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies   Valerie Obenchain
• [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies   Valerie Obenchain
• [BioC] Bug in GenomicRanges precede/follow   Valerie Obenchain
• [BioC] Problem with nearest() in GenomicRanges   Valerie Obenchain
• [BioC] Problem with nearest() in GenomicRanges   Valerie Obenchain
• [BioC] lumi - construct a design matrix   Moshe Olshansky
• [BioC] technical replicates and lmFit error   Ommen Kloeke, A.E.E. van
• [BioC] ChIPpeakAnno   Ou, Jianhong
• [BioC] ChIPpeakAnno to find peaks nearest to miRNA   Ou, Jianhong
• [BioC] Getting the length of every element from a large CompressedIRangesList is slow   Hervé Pagès
• [BioC] question regarding using cummeRbund package   Hervé Pagès
• [BioC] question regarding using cummeRbund package   Hervé Pagès
• [BioC] IRanges: the width argument of the coverage function   Hervé Pagès
• [BioC] IRanges coverage integer limit?   Hervé Pagès
• [BioC] GappedAlignmentPairs requests   Hervé Pagès
• [BioC] IRanges coverage integer limit?   Hervé Pagès
• [BioC] Getting the length of every element from a large CompressedIRangesList is slow   Hervé Pagès
• [BioC] GappedAlignmentPairs requests   Hervé Pagès
• [BioC] GappedAlignmentPairs requests   Hervé Pagès
• [BioC] IRanges coverage integer limit?   Hervé Pagès
• [BioC] Biostring: print sequence alignment to file   Hervé Pagès
• [BioC] Biostring: print sequence alignment to file   Hervé Pagès
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   Hervé Pagès
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Hervé Pagès
• [BioC] Request to add the latest dog genome release to BSGenome   Hervé Pagès
• [BioC] HTqPCR Normalization   Carmen Palacios
• [BioC] ontoCompare   Agnes Paquet
• [BioC] EBImage Sample code errors   Gregoire Pau
• [BioC] edgeR, error in estimateCommonDisp   Lucia Peixoto
• [BioC] Using readBAM function in segmentSeq   James Perkins
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   James Perkins
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   James Perkins
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   James Perkins
• [BioC] Oligo package, possible bug in paCalls   James Perkins
• [BioC] Oligo package, possible bug in paCalls   James Perkins
• [BioC] HTqPCR Normalization   James Perkins
• [BioC] [LIMMA]lmFit with continuous predictor   Belinda Phipson
• [BioC] How to extract expressed genes from Affymetrix data   Belinda Phipson
• [BioC] Biostring: print sequence alignment to file   Martin Preusse
• [BioC] Biostring: print sequence alignment to file   Martin Preusse
• [BioC] [EDGER] Normalization issue   François RICHARD
• [BioC] EdgeR and libsize normalization   François RICHARD
• [BioC] Installation of XCMS / mzR failed   Johannes Raffler
• [BioC] Installation of XCMS / mzR failed   Johannes Raffler
• [BioC] Contrast Problem   Aditi Rambani
• [BioC] Contrast Problem   Aditi Rambani
• [BioC] Contrast Problem   Aditi Rambani
• [BioC] rtracklayer import.gff3 mangling scores   Tim Rayner
• [BioC] Rsamtools::countBam returning in correct counts   Hubert Rehrauer
• [BioC] Rsamtools::countBam returning in correct counts   Hubert Rehrauer
• [BioC] Download problems from GEO   James F. Reid
• [BioC] DEXSeq error   Alejandro Reyes
• [BioC] Pasilla Package   Alejandro Reyes
• [BioC] error in DEXSeq version 1.3.13   Alejandro Reyes
• [BioC] multicore and DEXSeq   Alejandro Reyes
• [BioC] Limma: how to obtain P values using method "global" for multiple testing   Ribeiro,Eduardo de Souza
• [BioC] Limma: how to obtain P values using method "global" for multiple testing   Ribeiro,Eduardo de Souza
• [BioC] Limma: how to obtain P values using method "global" for multiple testing   Ribeiro,Eduardo de Souza
• [BioC] edgeR dispersions   Mark Robinson
• [BioC] report a possible buy in edgeR   Mark Robinson
• [BioC] how to get normalized counts from edgeR   Mark Robinson
• [BioC] edgeR norm.factors NaN   Mark Robinson
• [BioC] Can the normalization factors be too far apart in EdgeR analyses?   Mark Robinson
• [BioC] EdgeR and libsize normalization   Mark Robinson
• [BioC] overview function of made4   Anja Rockstroh
• [BioC] BioPAX parsing   Oliver Ruebenacker
• [BioC] Affy mas5 scaling   Liat S
• [BioC] Affy mas5 scaling   Liat S
• [BioC] Row labels in a heatmap   Liat S
• [BioC] Survival analysis (hazard ratio calculation)   Natasha Sahgal
• [BioC] edgeR: generating a correct design matrix - multifactorial design   Natasha Sahgal
• [BioC] edgeR: generating a correct design matrix - multifactorial design   Natasha Sahgal
• [BioC] crlmm Illumina cdfName "human1mv1c" not valid   Robert Scharpf
• [BioC] Linkage Disequilibrium Analysis   Holger Schwender
• [BioC] DESeq analysis   Fatemehsadat Seyednasrollah
• [BioC] ShortRead package   Fatemehsadat Seyednasrollah
• [BioC] Illumnia Filtering   Fatemehsadat Seyednasrollah
• [BioC] Reproducibility in DESeq   Fatemehsadat Seyednasrollah
• [BioC] FW: Reproducibility in DESeq   Fatemehsadat Seyednasrollah
• [BioC] goseq installation - BiasedUrn is not available   steve Shen
• [BioC] Counting reads for edgeR or voom()   Wei Shi
• [BioC] Wig files?   Ed Siefker
• [BioC] Wig files?   Siefker, Ed B.
• [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?   Fraser Sim
• [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?   Fraser Sim
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   Lan Sky
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   Lan Sky
• [BioC] GOstats: get genes for correspondâ ing enriched GO term   Lan Sky
• [BioC] boxplot a big list?   Janet L Smith
• [BioC] Package Gviz: boxplot question   Tim Smith
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Tim Smith
• [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt   Tim Smith
• [BioC] Gviz : UcscTrack ..   Tim Smith
• [BioC] Interaction contrasts with RCBD with replicates   Gordon K Smyth
• [BioC] Interaction contrasts with RCBD with replicates   Gordon K Smyth
• [BioC] LIMMA paired T-test   Gordon K Smyth
• [BioC] Very Different group sizes in DE of two conditions   Gordon K Smyth
• [BioC] Producing MA plots for single channel agilent data   Gordon K Smyth
• [BioC] design model EdgeR   Gordon K Smyth
• [BioC] LIMMA paired T-test   Gordon K Smyth
• [BioC] Contrast Problem   Gordon K Smyth
• [BioC] Contrast Problem   Gordon K Smyth
• [BioC] edgeR and tagwise dispersion: overcorrection for multiple tests?   Gordon K Smyth
• [BioC] two channel data normalization limma   Gordon K Smyth
• [BioC] attachments   Gordon K Smyth
• [BioC] edgeR, glmLRT error   Gordon K Smyth
• [BioC] Limma Design for Paired Samples Question   Gordon K Smyth
• [BioC] technical replicates and lmFit error   Gordon K Smyth
• [BioC] Limma: how to obtain P values using method "global" for multiple testing   Gordon K Smyth
• [BioC] edge R- p-value   Gordon K Smyth
• [BioC] edgeR: design matrix for different condition   Gordon K Smyth
• [BioC] edgeR: design matrix for different condition   Gordon K Smyth
• [BioC] how to design a model matrix and test by edgeR   Gordon K Smyth
• [BioC] how to design a model matrix and test by edgeR   Gordon K Smyth
• [BioC] edgeR, glmLRT error   Gordon K Smyth
• [BioC] a warining from edgeR   Gordon K Smyth
• [BioC] edgeR: design matrix for different condition   Gordon K Smyth
• [BioC] Contrast Problem   Gordon K Smyth
• [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)   Josef Spidlen
• [BioC] DESeq installation problems   Devi Swain
• [BioC] Fwd: edgeR dispersions   Bogdan Tanasa
• [BioC] Fwd: edgeR dispersions   Bogdan Tanasa
• [BioC] edgeR dispersions   Bogdan Tanasa
• [BioC] ChIPpeakAnno   Bogdan Tanasa
• [BioC] ChIPpeakAnno   Bogdan Tanasa
• [BioC] question regarding using cummeRbund package   Dan Tenenbaum
• [BioC] goseq installation - BiasedUrn is not available   Dan Tenenbaum
• [BioC] affylmGUI/biocReposList() Problem   Dan Tenenbaum
• [BioC] affylmGUI/biocReposList() Problem   Dan Tenenbaum
• [BioC] BIoconductor AMI with R version 2.15.1   Dan Tenenbaum
• [BioC] BIoconductor AMI with R version 2.15.1   Dan Tenenbaum
• [BioC] DESeq installation problems   Dan Tenenbaum
• [BioC] Rsamtools installation error   Dan Tenenbaum
• [BioC] Installation Trouble for bioc packages (FunciSNP, RSNPper) for v 2.15.1 (64-pc-linux-gnu (64-bit))   Dan Tenenbaum
• [BioC] attachments   Dan Tenenbaum
• [BioC] Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15   Dan Tenenbaum
• [BioC] Library not loaded: /usr/local/lib/libgvc.5.dylib (Rgraphviz)   Dan Tenenbaum
• [BioC] Library not loaded: /usr/local/lib/libgvc.5.dylib (Rgraphviz)   Dan Tenenbaum
• [BioC] Install details for root level administrators   Dan Tenenbaum
• [BioC] EBImage Sample code errors   Dan Tenenbaum
• [BioC] EBImage Sample code errors   Dan Tenenbaum
• [BioC] Installation of XCMS / mzR failed   Dan Tenenbaum
• [BioC] multicore and DEXSeq   Dan Tenenbaum
• [BioC] multicore and DEXSeq   Dan Tenenbaum
• [BioC] crlmm Illumina cdfName "human1mv1c" not valid   Richard Thompson
• [BioC] Simple conceptual question   Djie Tjwan Thung
• [BioC] Counting reads for edgeR or voom()   Tim Triche, Jr.
• [BioC] How can I obtain gene name from chromosome location?   Tim Triche, Jr.
• [BioC] IRanges problem: findOverlaps   Tim Triche, Jr.
• [BioC] Clustering question   Tim Triche, Jr.
• [BioC] CQN normalization   Sermsawat Tunlaya-Anukit
• [BioC] correlation coefficient for microarray biological replicates   Barbara Uszczynska
• [BioC] affyPara - rmaPara fails using cdfname   Tobias Verbeke
• [BioC] Influence of expression correlation on false positive ratio   January Weiner
• [BioC] Influence of expression correlation on false positive ratio   January Weiner
• [BioC] Bioconductor package implementing the GOrilla algorithm   January Weiner
• [BioC] entrez gene summary   David Westergaard
• [BioC] XML package cannot be installed   David Westergaard
• [BioC] Problem with nearest() in GenomicRanges   Chris Whelan
• [BioC] Problem with nearest() in GenomicRanges   Chris Whelan
• [BioC] SRAdb: differences between the database and the NCBI website   Ben Woodcroft
• [BioC] R 2.15.1 ReadAffy error   David Wragg
• [BioC] R 2.15.1 ReadAffy error   David Wragg
• [BioC] R 2.15.1 ReadAffy error   David Wragg
• [BioC] R 2.15.1 ReadAffy error   David Wragg
• [BioC] ggbio   Xin Yang
• [BioC] ggbio   Xin Yang
• [BioC] ggbio   Xin Yang
• [BioC] read.maimages   Assa Yeroslaviz
• [BioC] Agilent arrays 2- or 1-color?   Assa Yeroslaviz
• [BioC] Agilent arrays 2- or 1-color?   Assa Yeroslaviz
• [BioC] Agilent arrays 2- or 1-color?   Assa Yeroslaviz
• [BioC] Agilent arrays 2- or 1-color?   Assa Yeroslaviz
• [BioC] ggbio   Tengfei Yin
• [BioC] ggbio   Tengfei Yin
• [BioC] ggbio   Tengfei Yin
• [BioC] How can I obtain gene name from chromosome location?   Yoo, Seungyeul
• [BioC] How can I obtain gene name from chromosome location?   Yoo, Seungyeul
• [BioC] How can I obtain gene name from chromosome location?   Yoo, Seungyeul
• [BioC] How can I identify the closest transcript from a chromosome coordinate?   Yoo, Seungyeul
• [BioC] (pack: GOSemSim) NA semantic similarities between gene clusters   Guangchuang Yu
• [BioC] Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15   Peng Yu
• [BioC] Library not loaded: /usr/local/lib/libgvc.5.dylib (Rgraphviz)   Peng Yu
• [BioC] Library not loaded: /usr/local/lib/libgvc.5.dylib (Rgraphviz)   Peng Yu
• [BioC] Why org.At.tair.db is named differently?   Peng Yu
• [BioC] Why org.At.tair.db is named differently?   Peng Yu
• [BioC] How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?   Peng Yu
• [BioC] ChIPpeakAnno to find peaks nearest to miRNA   Zhu, Lihua (Julie)
• [BioC] adding channels to beadarray ExpressionSetIllumina class to log transform beadsummary data   Abhineet Uppal [guest]
• [BioC] goTools: Error in goidvect[test] : invalid subscript type \'list\'   Brad Davis [guest]
• [BioC] ontoCompare   Brad Davis [guest]
• [BioC] Interaction contrasts with RCBD with replicates   Daniel [guest]
• [BioC] Pasilla Package   David Parrish [guest]
• [BioC] Re : Filtering of data   Deeksha [guest]
• [BioC] Re : zero dimension error while soft thresholding in wgcna   Deeksha Malhan [guest]
• [BioC] Bioinformatics Academic Coordinator Job Posting   Guille Vallejo [guest]
• [BioC] Download problems from GEO   Hendrik [guest]
• [BioC] EBImage installation problem on Linux   Jayangshu Saha [guest]
• [BioC] AffyID mapping question   Jiayi Hou [guest]
• [BioC] Coordinate Question for Rgraphviz   Jiayi Hou [guest]
• [BioC] How to distinguish two overlapped nodes   Jiayi Hou [guest]
• [BioC] Gviz, DataTrack, Group plotting   Jonas [guest]
• [BioC] Producing MA plots for single channel agilent data   Lesley Hoyles [guest]
• [BioC] Problem producing imageplot for Agilent data   Lesley Hoyles [guest]
• [BioC] help needed - 7 array time course gene expression no replicates - fold change calculation   Liat [guest]
• [BioC] multicore and DEXSeq   Lynn Amon [guest]
• [BioC] two channel data normalization limma   Maite Iriondo [guest]
• [BioC] (pack: GOSemSim) NA semantic similarities between gene clusters   Manuel A.Alonso Tarajano [guest]
• [BioC] Very Different group sizes in DE of two conditions   Moriah [guest]
• [BioC] Rsamtools installation error   Murli [guest]
• [BioC] Reading Paired End Native Report Format in ShortRead   Murli Nair [guest]
• [BioC] #Identify differentially expressed genes   Paolo [guest]
• [BioC] agilent aCGH analysis   Preethi Sankaranarayanan [guest]
• [BioC] Coverage of reads per base position from BAM files   Rithun Mukherjee [guest]
• [BioC] LIMMA -- obtaining values used to calculate lfc   Sam McInturf [guest]
• [BioC] Illumina Average intensities with negative values   Sekaran [guest]
• [BioC] Help on invariantset normalization function   Sophie LAMARRE [guest]
• [BioC] reading fasta file into R   Tahir Mujtaba [guest]
• GOstats: get genes for correspondâ ing enriched GO term   Tim [guest]
• [BioC] question about RamiGO adjM2gml   Tim [guest]
• [BioC] XML package cannot be installed   Wayne Zhang [guest]
• [BioC] How to find frequent sequences.   vineet shukla [guest]
• [BioC] Download problem with GEOquery::getGEO()   axel.klenk at actelion.com
• [BioC] LIMMA paired T-test   somnath bandyopadhyay
• [BioC] LIMMA paired T-test   somnath bandyopadhyay
• [BioC] FARMS package   somnath bandyopadhyay
• [BioC] plier package   somnath bandyopadhyay
• [BioC] CMA package   somnath bandyopadhyay
• [BioC] Request to add the latest dog genome release to BSGenome   holly beale
• [BioC] Bioconductor Digest, Vol 113, Issue 28   bodenhofer at bioinf.jku.at
• [BioC] IRanges problem: findOverlaps   alessandro brozzi
• [BioC] design model EdgeR   chris_utah
• [BioC] Help with GSEAlm   b1gorsuch at comcast.net
• [BioC] Error fom XPS installation   cstrato
• [BioC] Exporting in XPS   cstrato
• [BioC] Bug in GenomicRanges precede/follow   a.statham at garvan.org.au
• [BioC] edgeR and tagwise dispersion: overcorrection for multiple tests?   alessandro.guffanti at genomnia.com
• [BioC] Calculate heterozygosity % using SNP genotype data   gowtham
• [BioC] Calculate heterozygosity % using SNP genotype data   gowtham
• [BioC] Calculate heterozygosity % using SNP genotype data   gowtham
• [BioC] Calculate heterozygosity % using SNP genotype data   gowtham
• [BioC] Limma topTable; fold changes look completely different to the normalized data and Limma fold change   john herbert
• [BioC] Limma topTable; fold changes look completely different to the normalized data and Limma fold change   john herbert
• [BioC] Limma topTable; fold changes look completely different to the normalized data and Limma fold change   john herbert
• [BioC] Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15   wenhuo hu
• [BioC] Testing for no difference   jones
• [BioC] boxplot a big list?   John linux-user
• [BioC] edgeR norm.factors NaN   Davenport.Colin at mh-hannover.de
• [BioC] How to extract expressed genes from Affymetrix data   michelle_low
• [BioC] How to extract expressed genes from Affymetrix data   michelle_low
• [BioC] design matrix edge R pairwise comparison at different timepoints after infection with replicates   wang peter
• [BioC] about edgeR   wang peter
• [BioC] report a problem of DESeq   wang peter
• [BioC] report a problem of DESeq   wang peter
• [BioC] report a possible buy in edgeR   wang peter
• [BioC] how to get normalized counts from edgeR   wang peter
• [BioC] what is the default parameters of estimateDispersions in the DESeq   wang peter
• [BioC] what is the default parameters of estimateDispersions in the DESeq   wang peter
• [BioC] how to design model in DESeq   wang peter
• [BioC] DESeq and contrasts   wang peter
• [BioC] how to design comparision using edgeR   wang peter
• [BioC] how to design comparision using edgeR   wang peter
• [BioC] any package can map transcripts to GO   wang peter
• [BioC] how to design comparision using edgeR   wang peter
• [BioC] how to count for edgeR input   wang peter
• [BioC] how to design a model matrix and test by edgeR   wang peter
• [BioC] a possible bug in DESeq   wang peter
• [BioC] how to design a model matrix and test by edgeR   wang peter
• [BioC] a warining from edgeR   wang peter
• [BioC] a possible bug in DESeq   wang peter
• [BioC] a warining from edgeR   wang peter
• [BioC] how to do GO analysis if i have some sequences   wang peter
• [BioC] GOstats adding custom annotations   sudeep s
• [BioC] help   rakesh sharma
• [BioC] Interaction contrasts with RCBD with replicates   dantayrod at stat.ufl.edu
• [BioC] Question regarding cellhts2 output   maziz at tgen.org
• [BioC] Question regarding cellhts2 output   maziz at tgen.org
• [BioC] function for inverse normal transformation   carol white
• [BioC] microarray box-plot   jiqiang yao
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   shirley zhang
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   shirley zhang
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   shirley zhang
• [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array   shirley zhang
• [BioC] Limma Design for Paired Samples Question   zeynep özkeserli
• [BioC] Limma Design for Paired Samples Question   zeynep özkeserli

Last message date: Tue Jul 31 21:48:17 CEST 2012
Archived on: Thu Aug 2 08:04:00 CEST 2012

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