July 2012 Archives by thread
Starting: Sun Jul 1 02:45:34 CEST 2012
Ending: Tue Jul 31 21:48:17 CEST 2012
Messages: 631
- [BioC] R 2.15.1 ReadAffy error
Henrik Bengtsson
- [BioC] question regarding using cummeRbund package
Jack Luo
- [BioC] crlmm Illumina cdfName "human1mv1c" not valid
Richard Thompson
- [BioC] HTqPCR plotting groups of interest
Simon Melov
- [BioC] overview function of made4
Anja Rockstroh
- [BioC] Re : zero dimension error while soft thresholding in wgcna
Deeksha Malhan [guest]
- [BioC] AffyID mapping question
Jiayi Hou [guest]
- [BioC] Help on invariantset normalization function
Sophie Lamarre
- [BioC] Interaction contrasts with RCBD with replicates
Daniel [guest]
- [BioC] Illumina Average intensities with negative values
Sekaran [guest]
- [BioC] Getting the length of every element from a large CompressedIRangesList is slow
Nicolas Delhomme
- [BioC] Surrogate variable analysis fails with “subscript out of bounds”
Vebjorn Ljosa
- [BioC] Coordinate Question for Rgraphviz
Jiayi Hou [guest]
- [BioC] easyRNAseq question
Akula, Nirmala (NIH/NIMH) [C]
- [BioC] design model EdgeR
chris_utah
- [BioC] goseq installation - BiasedUrn is not available
steve Shen
- [BioC] AnnotationDbi: NewSchema vignette error
Mark Cowley
- [BioC] HTqPCR problems
Heidi Dvinge
- [BioC] miRNA exiqon panels and HTqPCR
Heidi Dvinge
- [BioC] Very Different group sizes in DE of two conditions
Moriah [guest]
- [BioC] Using readBAM function in segmentSeq
James Perkins
- [BioC] DESeq analysis
Fatemehsadat Seyednasrollah
- [BioC] Counting reads for edgeR or voom()
Cittaro Davide
- [BioC] GenomicRanges: nearest() for GRanges not returning overlaps
James Perkins
- [BioC] IRanges: the width argument of the coverage function
Nicolas Delhomme
- [BioC] IRanges coverage integer limit?
Nicolas Delhomme
- [BioC] Re : Filtering of data
Deeksha [guest]
- [BioC] Error message running through CQN Vignette
Richard Friedman
- [BioC] SWAN normalization for HumanMethylation450K - minfi
Lucia Lam
- [BioC] Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays
Karthik K N
- [BioC] Another question about normalization of data
Gustavo Fernández Bayón
- [BioC] Oligo package, possible bug in paCalls
James Perkins
- [BioC] Producing MA plots for single channel agilent data
Lesley Hoyles [guest]
- [BioC] missing figure text in arrayQualityMetrics
Daniel Aaen Hansen
- [BioC] nem package, nem.BN learning with 'continuous_Baysian' not possible
Siebourg Juliane
- [BioC] Job offer: Computational Biologist, Oncology Novartis
Kauffmann, Audrey
- [BioC] reads of different lengths (easyRNASeq)
Nicolas Delhomme
- [BioC] pathway ID in KEGG.db
Ed
- [BioC] DEseq and FDR correction
Wolfgang Huber
- [BioC] Rsamtools::countBam returning in correct counts
Hubert Rehrauer
- [BioC] Linkage Disequilibrium Analysis
Ovokeraye Achinike-Oduaran
- [BioC] affylmGUI/biocReposList() Problem
Burkhard Heil
- [BioC] Error fom XPS installation
Liu, Binbin
- [BioC] Help with GSEAlm
b1gorsuch at comcast.net
- [BioC] design matrix edge R pairwise comparison at different timepoints after infection with replicates
wang peter
- [BioC] Problems with iteration (sappily) over RNAStringSet
Kemal Akat
- [BioC] Converting floating point RangedData to Rle
Marcin Imielinski
- [BioC] about edgeR
wang peter
- [BioC] ShortRead package
Fatemehsadat Seyednasrollah
- [BioC] Illumnia Filtering
Fatemehsadat Seyednasrollah
- [BioC] DEXSeq error
Chuming Chen
- [BioC] Problems with ggbio
Michael Muratet
- [BioC] goTools: Error in goidvect[test] : invalid subscript type \'list\'
Brad Davis [guest]
- [BioC] report a problem of DESeq
wang peter
- [BioC] Fwd: edgeR dispersions
Bogdan Tanasa
- [BioC] Rsamtools: Read a bam line by line
Alex Gutteridge
- [BioC] ChIPpeakAnno
Bogdan Tanasa
- [BioC] down-expression and high-expression in single cell + amplification
Dror Hibsh
- [BioC] report a possible buy in edgeR
wang peter
- [BioC] how to get normalized counts from edgeR
wang peter
- [BioC] Influence of expression correlation on false positive ratio
January Weiner
- [BioC] Survival analysis (hazard ratio calculation)
Farscape2012
- [BioC] Bioconductor package implementing the GOrilla algorithm
January Weiner
- [BioC] How can I obtain gene name from chromosome location?
Yoo, Seungyeul
- [BioC] Contrast Problem
Aditi Rambani
- [BioC] GappedAlignmentPairs requests
Hervé Pagès
- [BioC] Download problem with GEOquery::getGEO()
axel.klenk at actelion.com
- [BioC] help needed - 7 array time course gene expression no replicates - fold change calculation
Liat [guest]
- [BioC] Download problems from GEO
Hendrik [guest]
- [BioC] Problem with R453Plus1 Toolbox and files from a Roche GS Junior
Olivia Jardin-Mathé
- [BioC] DESeq installation problems
Devi Swain
- [BioC] IRanges problem: findOverlaps
Nicolas DESCOSTES
- [BioC] Basic question about analysis of unbalanced design in microarray experiment
Guido Leoni
- [BioC] GO enrichment significance
Grimes Mark
- [BioC] BIoconductor AMI with R version 2.15.1
Jeff Knisley
- [BioC] minor allele frequency comparison from two softwares based on the same sequencing data
Jiafen
- [BioC] SRAdb: differences between the database and the NCBI website
Ben Woodcroft
- [BioC] regenerate CEL file from analyzed data
J. Greenbaum
- [BioC] expression status from pvalues
Alyaa Mahmoud
- [BioC] Reproducibility in DESeq
Fatemehsadat Seyednasrollah
- [BioC] Clustering question
Gustavo Fernández Bayón
- [BioC] EBImage installation problem on Linux
Jayangshu Saha [guest]
- [BioC] comparing qpcr and chip
Marco Fabbri
- [BioC] problems reading fcs files / flowcore / read.fcs
David Corne
- [BioC] two channel data normalization limma
Maite Iriondo
- [BioC] what is the default parameters of estimateDispersions in the DESeq
wang peter
- [BioC] Selecting elements in GRanges object by element metadata
Michael Muratet
- [BioC] Rsamtools installation error
Murli [guest]
- [BioC] Pasilla Package
David Parrish [guest]
- [BioC] how to design model in DESeq
wang peter
- [BioC] edgeR and tagwise dispersion: overcorrection for multiple tests?
alessandro.guffanti at genomnia.com
- [BioC] #Identify differentially expressed genes
Paolo [guest]
- [BioC] flowQ loading issue
Fletez-Brant, Christopher (NIH/VRC) [C]
- [BioC] problems reading fcs files / flowcore / read.fcs (David Corne)
Finak, Greg
- [BioC] Affy mas5 scaling
Liat S
- [BioC] ontoCompare
Brad Davis [guest]
- [BioC] Reading Paired End Native Report Format in ShortRead
Murli Nair [guest]
- [BioC] Wig files?
Ed Siefker
- [BioC] [LIMMA]lmFit with continuous predictor
Yao Chen
- [BioC] How to find frequent sequences.
vineet shukla [guest]
- [BioC] Installation Trouble for bioc packages (FunciSNP, RSNPper) for v 2.15.1 (64-pc-linux-gnu (64-bit))
Timothy Duff
- [BioC] help with genotyping
Pina Iannelli
- [BioC] Bioc 2012 Schedule
Martin Morgan
- [BioC] DESeq and contrasts
wang peter
- [BioC] Question regarding cellhts2 output
maziz at tgen.org
- [BioC] affyPara - rmaPara fails using cdfname
Tobias Verbeke
- [BioC] exomeCopy - no .Internal function 'cov' error
Lescai, Francesco
- [BioC] College bioinformatics project suggestions?
Caitlin
- [BioC] edgeR, glmLRT error
Cei Abreu-Goodger
- [BioC] Translating AB/BB/AA into a SNP with Illumina data
Lavinia Gordon
- [BioC] Limma Design for Paired Samples Question
zeynep özkeserli
- [BioC] Row labels in a heatmap
Liat S
- [BioC] access Limma objects
Chuming Chen
- [BioC] rtracklayer import.gff3 mangling scores
Tim Rayner
- [BioC] Is it recommended to remove control probes for Agilent type data
Ketaki
- [BioC] BiomaRt - Flanking regions
Ovokeraye Achinike-Oduaran
- [BioC] DiffBind error with DBA_DESEQ_GLM and warning with DBA_EDGE_GLM
Elisabetta Manduchi
- [BioC] Bioinformatics Academic Coordinator Job Posting
Guille Vallejo [guest]
- [BioC] limma voom: How to create double contrasts?
Christian Ametz
- [BioC] Bioc Interface for 1,000 Genomes SNP Frequencies
Timothy Duff
- [BioC] CQN normalization
Sermsawat Tunlaya-Anukit
- [BioC] microarray box-plot
jiqiang yao
- [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?
Fraser Sim
- [BioC] Coverage of reads per base position from BAM files
Rithun Mukherjee [guest]
- [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] Install details for root level administrators
Paul Johnson
- [BioC] illuminaHumanv4.db missing keys in last version
Amos Kirilovsky
- [BioC] Problem producing imageplot for Agilent data
Lesley Hoyles [guest]
- [BioC] how to design comparision using edgeR
wang peter
- [BioC] EasyRNASeq issue (missing bai files)
Nicolas Delhomme
- [BioC] any package can map transcripts to GO
wang peter
- [BioC] EBImage Sample code errors
Robert Baer
- [BioC] obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
shirley zhang
- [BioC] Bug in GenomicRanges precede/follow
a.statham at garvan.org.au
- [BioC] Biostring: print sequence alignment to file
Hervé Pagès
- [BioC] Simple conceptual question
Gustavo Fernández Bayón
- [BioC] technical replicates and lmFit error
Ommen Kloeke, A.E.E. van
- [BioC] edgeR norm.factors NaN
Davenport.Colin at mh-hannover.de
- [BioC] plier package
somnath bandyopadhyay
- [BioC] counts from HTSeq vs DEXSeq
Akula, Nirmala (NIH/NIMH) [C]
- [BioC] ReadVcf Memory Issues
Timothy Duff
- [BioC] How can I identify the closest transcript from a chromosome coordinate?
Yoo, Seungyeul
- [BioC] function for inverse normal transformation
carol white
- [BioC] [EDGER] Normalization issue
François RICHARD
- [BioC] Calculate heterozygosity % using SNP genotype data
gowtham
- [BioC] Can the normalization factors be too far apart in EdgeR analyses?
Hoskins, Jason (NIH/NCI) [F]
- GOstats: get genes for correspondâ ing enriched GO term
Tim [guest]
- [BioC] Limma: how to obtain P values using method "global" for multiple testing
Ribeiro,Eduardo de Souza
- [BioC] adding channels to beadarray ExpressionSetIllumina class to log transform beadsummary data
Abhineet Uppal [guest]
- [BioC] question about RamiGO adjM2gml
Tim [guest]
- [BioC] edge R- p-value
chris Jhon
- [BioC] How to extract expressed genes from Affymetrix data
michelle_low
- [BioC] Testing for no difference
Gustavo Fernández Bayón
- [BioC] GOstats adding custom annotations
sudeep s
- [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
Karthik K N
- [BioC] Package Gviz: boxplot question
Tim Smith
- [BioC] lumi - construct a design matrix
Paolo Kunderfranco
- [BioC] correlation coefficient for microarray biological replicates
Barbara Uszczynska
- [BioC] how to count for edgeR input
wang peter
- [BioC] BioPAX parsing
Oliver Ruebenacker
- [BioC] Gviz : UcscTrack ..
Tim Smith
- [BioC] Registration is now open for COMBINE 2012. Aug.15-19 in Toronto, Canada
Robin Haw
- [BioC] (pack: GOSemSim) NA semantic similarities between gene clusters
Manuel A.Alonso Tarajano [guest]
- [BioC] EdgeR and libsize normalization
François RICHARD
- [BioC] reading fasta file into R
Tahir Mujtaba [guest]
- [BioC] edgeR: design matrix for different condition
KJ Lim
- [BioC] Why org.At.tair.db is named differently?
Peng Yu
- [BioC] entrez gene summary
Amit Kumar Kashyap
- [BioC] Warnings with running easyRNASeq with easyRNASeq tutorial
Richard Friedman
- [BioC] Request to add the latest dog genome release to BSGenome
holly beale
- [BioC] Normalization of array leads to decrease in number of differentially expressed genes
Cytochalasin
- [BioC] Exporting in XPS
Lavorgna Giovanni
- [BioC] HTqPCR Normalization
Carmen Palacios
- [BioC] how to design a model matrix and test by edgeR
wang peter
- [BioC] undocumented behavior in tilingArray::costMatrix [Scanned]
Du, Yang
- [BioC] Why does a call to "unique" removes a DNAStringSet names?
Nicolas Delhomme
- [BioC] error in DEXSeq version 1.3.13
Akula, Nirmala (NIH/NIMH) [C]
- [BioC] Gviz, DataTrack, Group plotting
Jonas [guest]
- [BioC] a possible bug in DESeq
wang peter
- [BioC] How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?
Peng Yu
- [BioC] ChIPpeakAnno - Annotation of miRNA
Paolo Kunderfranco
- [BioC] ChIPpeakAnno to find peaks nearest to miRNA
Paolo Kunderfranco
- [BioC] LIMMA -- obtaining values used to calculate lfc
Sam McInturf [guest]
- [BioC] agilent aCGH analysis
Preethi Sankaranarayanan [guest]
- [BioC] draw path-diagram Rgraphvis
René Mayer
- [BioC] XML package cannot be installed
Wayne Zhang [guest]
- [BioC] Bioconductor Digest, Vol 113, Issue 28
bodenhofer at bioinf.jku.at
- [BioC] Help with choice of normalization
Cytochalasin
- [BioC] Problem with nearest() in GenomicRanges
Chris Whelan
- [BioC] a warining from edgeR
wang peter
- [BioC] edgeR- data for case studies
Johnson, Franklin Theodore
- [BioC] FARMS package (fwd)
Günter Klambauer
- [BioC] DiffBind error loading dba.count
Paolo Kunderfranco
- [BioC] Installation of XCMS / mzR failed
Johannes Raffler
- [BioC] read.maimages
Assa Yeroslaviz
- [BioC] lumi - limma - geneSymbol/geneName
Paolo Kunderfranco
- [BioC] edgeR, error in estimateCommonDisp
Lucia Peixoto
- [BioC] limma time course analysis userguide example for two color microarray
Maite Iriondo
- [BioC] Agilent arrays 2- or 1-color?
Assa Yeroslaviz
- [BioC] multicore and DEXSeq
Lynn Amon [guest]
- [BioC] general question about omogeneity of variances between microarray groups
Guido Leoni
- [BioC] help
rakesh sharma
- [BioC] How to distinguish two overlapped nodes
Jiayi Hou [guest]
- [BioC] how to do GO analysis if i have some sequences
wang peter
- [BioC] clarification on DEXSeq output
Akula, Nirmala (NIH/NIMH) [C]
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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