April 2014 Archives by thread
Starting: Tue Apr 1 00:05:43 CEST 2014
Ending: Wed Apr 30 23:56:42 CEST 2014
Messages: 603
- [BioC] MEDIPS.createSet error
Vining, Kelly
- [BioC] SomaticSignatures
Dan Tenenbaum
- [BioC] DEXSeq dispersion trend estimation?
Alejandro Reyes
- [BioC] Query
swathi mutyam
- [BioC] Running the GSEA algorithm
Leif Väremo
- [BioC] Voom Normalization and negative numbers
Michael Breen
- [BioC] annotating the results with association gene symbol
Rabia [guest]
- [BioC] detecting oscillating genes from RNA-seq data
mali salmon
- [BioC] countOverlaps gives an empty SummarizeExperiments
Rafael Viana [guest]
- [BioC] Choosing the kernel for SVM (regression) using rminer package
Paul [guest]
- [BioC] Bioconductor newsletter: April 2014
Valerie Obenchain
- [BioC] DiffBind
Rory Stark
- [BioC] Limitations in edgeR?
Eleanor Su
- [BioC] Designing a model with blocking and other interactions
Eleanor Su
- [BioC] A question about the function readGAlignmentPairs in GenomicRnages package
Niu, Liang (NIH/NIEHS) [E]
- [BioC] Rsamtools filtering bam file: RE: MEDIPS.createSet error
Vining, Kelly
- [BioC] Job: PhD and postdoc position at DKFZ Heidelberg
Bernd Fischer
- [BioC] queries re Voom + Limma for RNA-seq data
Gordon K Smyth
- [BioC] Join expression values of replicas in edgeR
Gordon K Smyth
- [BioC] BiocLite eror
Rabia Johnson
- [BioC] RamiGO package function getAmigoTree broken
Asta Laiho
- [BioC] So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Vining, Kelly
- [BioC] Problem acessing indexed information in hdf5 database
Maria Pedroto
- [BioC] justRMA (package Affy) messing up phenoData when passing an AnnotatedDataFrame
Arnaud
- [BioC] Error working with indexes in htf5 files
Maria Pedroto [guest]
- [BioC] rtracklayer export: enable trackline for GRanges and RleLists, etc?
Janet Young
- [BioC] About ChIPpeakAnno output = "shortestDistance"
Zhu, Lihua (Julie)
- [BioC] DiffBind counts
Naomi Altman
- [BioC] oligo annotation: pd.mogene.2.0.st vs pd.mogene.2.0.st.v1
Bernd Klaus
- [BioC] extracting CPM from a DGElist after normalization in edgeR
alessandro.guffanti at genomnia.com
- [BioC] DEXSeq output - count file
Alejandro Reyes
- [BioC] MethyLumiM to MethyLumiSet?
Victoria Svinti
- [BioC] It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Vining, Kelly
- [BioC] small GWASTools patch to allow to use already built gds objects in Genotype Readers
Karl Forner
- [BioC] Starr package: cmarrt.ma error
Paul
- [BioC] EdgeR repeated measurment
teshe [guest]
- [BioC] IdeogramTrack and bigWig file errors in Gviz
Robert Ivanek
- [BioC] package affy / biobase problem with function "geneNames"
BEN HAMDA Cherif
- [BioC] DESeq2
aroa [guest]
- [BioC] Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9)
Dan Tenenbaum
- [BioC] CHARM qcReport Question
zeynep özkeserli
- [BioC] Factor-related problem when creating new flowFrame
Kipper Fletez-Brant
- [BioC] Deseq2-help
Michael Love
- [BioC] edgeR
Jahn Davik [guest]
- [BioC] logFC , Limma (microArray Analysis)
BEN HAMDA Cherif
- [BioC] Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Ed O'Donnell [guest]
- [BioC] Trying to use BSgenome.Hsapiens.NCBI.GRCh38
Hervé Pagès
- [BioC] Changelog for DESeq2 1.2.10 ?
Carl Herrmann
- [BioC] BiomaRt getBM error: Unknown column
Yury Bukhman [guest]
- [BioC] How to reduce two GRanges simutaneously
Niu, Liang (NIH/NIEHS) [E]
- [BioC] Downloading Multiple Genome Alignments from UCSC Genome Browser
Manuel Razo-Mejia [guest]
- [BioC] Feature request for Rsubread::featureCounts: read length adjustment
Ryan C. Thompson
- [BioC] VariantAnnotation - extracting AD and PL fields
Lavinia Gordon
- [BioC] CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide arrays)
Joan [guest]
- [BioC] WGCNA package
amit kumar subudhi
- [BioC] Announcement: (Free) Course 29-30 May, HPC Wales: Parallel Computing with R using SPRINT on post-genomic data
SPRINT Project
- [BioC] GEOquerry and virtualArray
Blumenberg, Miroslav
- [BioC] Getting edgeR normalized counts within the GLM approach
Mathieu Bahin
- [BioC] unsuscribe
Sean MacEachern
- [BioC] KEGG pathway analysis with ReportingTools
Mayte Suarez-Farinas
- [BioC] What is the easiest way to make the GC content and length matrix for package cqn?
Thornton, Matthew
- [BioC] Inquiries of rhdf5
Bernd Fischer
- [BioC] rehh package for iHS and Rsb
Abugri James
- [BioC] affy( ) error with mas5()
Ying Chen
- [BioC] biocLite installing to tmp directory
NAOMI S ALTMAN
- [BioC] DEXSeq- dexseq_prepare_annotation.py error
Anitha Sundararajan
- [BioC] question about output of edgeR
Son Pham
- [BioC] installing flowDensity
Raghu
- [BioC] what is the difference between org.Hs.eg.dbGO2EG and org.Hs.eg.dbGO2ALLEGS?
Zhishi Wang
- [BioC] trying to get TeX or LaTeX for R 3.0.3
judyh [guest]
- [BioC] Making three-way and four-way comparisons
Maria [guest]
- [BioC] Bioconductor Digest, Vol 134, Issue 10
Mike
- [BioC] RangedData change space information
Radhouane Aniba
- [BioC] DESeq2: Paired Test
Pankaj Agarwal
- [BioC] GOseq with ce6
François Lefebvre
- [BioC] Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo package)
Tommaso Raffaello
- [BioC] GOSemSim with mgoSim results changed based on the order of input GO terms
Matt McNeill [guest]
- [BioC] easyRNASeq: Number of total counts
Pankaj Agarwal [guest]
- [BioC] Substitution for edd package
594898865
- [BioC] voom transformed data
Gokmen [guest]
- [BioC] doParallel with Bumphunter gives Error in mcfork()
Brad Ruzicka [guest]
- [BioC] package "affy" & "simpleaffy"
BEN HAMDA Cherif
- [BioC] phyloseq/DESeq gives negative transformed values
Sophie Josephine Weiss
- [BioC] GenomicFeatures: Problem with makeTranscriptDbFromGFF
Katja Hebestreit
- [BioC] Interpretation of fold.changes for covariates in a linear model using voom
Francesco Gatto [guest]
- [BioC] miRNA to gene mapping (miRNApath)
Kishor Tappita
- [BioC] R 3.1.0 and dexseq 1.8.0
Rao,Xiayu
- [BioC] unknown error in DiffBind package
Roberta Sanfilippo [guest]
- [BioC] Phyloseq/DEseq transformed data
Susan Holmes
- [BioC] GWASdata
Naomi Altman
- [BioC] Bioconductor 2.14 is released
Dan Tenenbaum
- [BioC] how to close a hdf5 file
Uday Maitra [guest]
- [BioC] DEseq() takes extremely long time
Michael Love
- [BioC] summarizeOverlaps using GRanges or bed file as reads?
Ryan C. Thompson
- [BioC] lumi - limma contrast design
Paolo Kunderfranco
- [BioC] limma modeling, paired samples and continuous variable
michela riba [guest]
- [BioC] Limma table results
Stefania [guest]
- [BioC] Problem installing latest Bioconductor version
Leena Kytömäki [guest]
- [BioC] Indexing an RleList by GRanges
Johnston, Jeffrey
- [BioC] Which log2FC to report?
Rafael Moreira [guest]
- [BioC] TCC::ERROR: Need the design matrix for GLM.
Pankaj Agarwal
- [BioC] Can\'t load new BioC packages
David Lapointe [guest]
- [BioC] About ChIPpeakAnno
Lucia Peixoto
- [BioC] dexseq read.HTSeqCounts error
Rao,Xiayu
- [BioC] Help with error when trying to run browserView from rtracklayer
John Brothers [guest]
- [BioC] use of voom function with attract package
Emmanouela Repapi [guest]
- [BioC] GWAS with family data
Naomi Altman
- [BioC] Rgraphviz compilation error
Venkat Seshan [guest]
- [BioC] fRMA- more issues with custom CDFs
Cornwell, Adam
- [BioC] edgeR and calcNormFactors manually
Scott Daniel
- [BioC] singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
Sean Li [guest]
- [BioC] Rgraphviz install problem.HELP!!!!!
leo [guest]
- [BioC] older version of org.Hs.eg.db
1frcn [guest]
- [BioC] Error in isVersioned(object)
Joachim Schumann [guest]
- [BioC] flowCore package - logicle transformation
Mike
- [BioC] help needed with the design matrix
Nair [guest]
- [BioC] Looking for a function
Jerry Cholo
- [BioC] Fontconfig error in R 3.10 when running
Yue Li
- [BioC] Help with sliding window analysis on GRanges object
Vince S. Buffalo
- [BioC] Problems using intansv...
Phil Ross
- [BioC] strange spam from biocbuild
Marc Carlson
- [BioC] TCC::ERROR: Need the design matrix for GLM
Gordon K Smyth
- [BioC] Rsamtools - summarizeOverlaps - count read on complementary strand
samuel collombet [guest]
- [BioC] logFC and CPM of edgeR
Shuhei Yao [guest]
- [BioC] Ontology lack in goProfiles : no BP or CC just MF
Arnaud Mounier
- [BioC] Warnings after gcrma normalisation...
Bas Jansen
- [BioC] Question about the ChIPpeakAnno:
Zhu, Lihua (Julie)
- [BioC] Limma table results [time course analysis]
Gordon K Smyth
- [BioC] Counterintuitive results from edgeR
Son Pham
- [BioC] The installation of XVector
GUAN Rui [guest]
- [BioC] problem with \"readCufflinks\"
Peng [guest]
- [BioC] Blast analysis of two sequences in R
prabhakar ghorpade
- [BioC] 答复: problem with \"readCufflinks\"
Dan Tenenbaum
- [BioC] countOverlaps Warnings
Pankaj Agarwal
- [BioC] RNA seq
Minni [guest]
- [BioC] dexseq fitDispersionFunction(ecs) error
Rao,Xiayu
- [BioC] preprocess core for quantile normalization
Yashwant
- [BioC] normalization
Yashwant Kumar
- [BioC] Comparison of murine and human microarray data
Bas van Gestel
- [BioC] Testing sensitivity and specificity on random biological sequence
Jiří Hon
- [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Leonardo Collado Torres
- [BioC] MLSeq Mathematical Concepts
Dario Strbenac
- [BioC] ChIPpeakAnno
Paolo Kunderfranco
- [BioC] Elephant shark genome
Miguel [guest]
- [BioC] summarizeOverlaps: number of dropped reads
Gabriele Schweikert
- [BioC] 答复: 答复: problem with \"readCufflinks\"
Dan Tenenbaum
- [BioC] EdgeR: dispersion estimation
Yanzhu [guest]
- [BioC] Affymetrix HTA 2 array analysis
Elena Serrano
- [BioC] EdgeR: replicated pools, yes or not?
Manuel J Gómez [guest]
- [BioC] dmpFinder method question
Giovanni Calice
- [BioC] ReportingTools problem with GO report
Assa Yeroslaviz
- [BioC] dmpFinder Gene ID question
Giovanni Calice
- [BioC] ReportingTools gene IDs
Assa Yeroslaviz
- [BioC] DESeq2 16S copy number correction
Manoeli Lupatini
- [BioC] Plotting per base coverage from genomecoveragebed utility
VG
- [BioC] Unsubscribe me from list
Abugri James
- [BioC] Pathview question
Luo Weijun
- [BioC] ERROR: No residual degrees of freedom in linear model fits
jesus urbano
- [BioC] edgeR - paired samples with multifactorial design - errors
Preethy [guest]
- [BioC] Draft support for HTA 2.0 with oligo
Elena Serrano
- [BioC] hclust and cutree
chris Jhon
- [BioC] ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0
Guan
- [BioC] Remove batch effect in small RNASeq study (SVA or others?)
shirley zhang
- [BioC] Genes Symbols lists question
Giovanni Calice
- [BioC] 答复: 答复: 答复: problem with \"readCufflinks\"
Dan Tenenbaum
- [BioC] Unknown failure in virtualArrayLoadRaw
Robert Soeldner [guest]
- [BioC] Odd Odds Ratio in GOstats package
Moreno Colaiacovo
- [BioC] error when using waveTiling package
chris blazier
- [BioC] RGraphiz installation keeps on failing ubuntu 12.04 LTS server
Frederiek - Maarten Kerckhof [guest]
- [BioC] inSilicoMerging:::mergeCOMBAT covariates
François Lefebvre
- [BioC] package for iAUC determination using gene expression data?
Hooiveld, Guido
- [BioC] limma small vs large number of samples
Giovanni Bucci
- [BioC] Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Brian Herb
- [BioC] GEOquery/virtualArray package error
Nafiseh Saberian [guest]
- [BioC] Strange error using the \"narrow\" function for a ShortReadQ object
Tomas Bjorklund [guest]
- [BioC] how to set up sampleInfo for methylation array in illumina 450K
guest [guest]
- [BioC] Insignificant q-values in minfi
kaushal Raj Chaudhary [guest]
- [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization
Stefanie Busch
- [BioC] total count filter cutoff
mahnaz Kiani [guest]
- [BioC] Gviz AnnotationTrack - Consistent y-scales
Lance Parsons
Last message date:
Wed Apr 30 23:56:42 CEST 2014
Archived on: Thu May 1 00:02:11 CEST 2014
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