March 2010 Archives by thread
Starting: Mon Mar 1 02:56:27 CET 2010
Ending: Wed Mar 31 23:37:22 CEST 2010
Messages: 623
- [BioC] GO's to gene's
Loren Engrav
- [BioC] pair information of microRNA and Targets prediction
jrwang at itri.org.tw
- [BioC] Search queries with biomaRt does not align with online queries via ensembl
Hotz, Hans-Rudolf
- [BioC] Porting RWebServices from Axis1 to Axis2
Michael Dondrup
- [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Mikhail Pachkov
- [BioC] Mapping using absolute coordinates
Ludo Pagie
- [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Mikhail Pachkov
- [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Mikhail Pachkov
- [BioC] how to use rtracklayer to retrieve sequence of list of coordinates
sabrina s
- [BioC] what is the website to get gene name from Affy probe set ID?
James Anderson
- [BioC] makePDpackage
somnath bandyopadhyay
- [BioC] makePDpackage
Benilton Carvalho
- [BioC] R package for analyzing MS/MS spectra
Kishor Tappita
- [BioC] Help on Cosmo
Prashantha Hebbar Kiradi [MU-MLSC]
- [BioC] Loop design - biological, technical replication and contrasts
Maciej Jończyk
- [BioC] COURSE: Microarray Analysis in R (Bioconductor) from Imperial College
North, Bernard V
- [BioC] getSeq error with multiple inqueries, BSgenome
sabrina s
- [BioC] affycomp updated in release branch
Harris A. Jaffee
- [BioC] GO's to gene's
Marc Carlson
- [BioC] GEOquery question -- suppressing download for GPL queries?
Sean Davis
- [BioC] landscape genetics analysis
milton ruser
- [BioC] heatmap for high number of genes
avehna
- [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6
Dick Beyer
- [BioC] R / R+ Webminar *** R-PLUS Rocks: Interactive, Comprehensible and Highly Visual. March 12th @ 12PM ET (USA Time)
sue at xlsolutions-corp.com
- [BioC] Help on Cosmo back ground model
Prashantha Hebbar
- [BioC] GEOquery not working, NCBI changes?
Gad Abraham
- [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6
Dick Beyer
- [BioC] PCA or concordance
Johnny H
- [BioC] R package for analyzing MS/MS spectra
Prashantha Hebbar
- [BioC] Xlaevis probe sequence file for gcRMA not found.
Naoki Irie
- [BioC] experience with rankproduct vs. limma - combining results
Hildebrand, Georg
- [BioC] retrieveGenomicFeatureAnnotation.R file supplied with Ringo
Paul Geeleher
- [BioC] ensembl annotation coordinate did not match that from UCSC genome browser using ucscTableQuery
sabrina s
- [BioC] Annotation for a GEO data set
Joern Grame
- [BioC] Using annotation maps as environments in packages
Antti Honkela
- [BioC] trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem
Andrew Yee
- [BioC] affyPara: background correction & normalization only?
Leo Lahti
- [BioC] hgu133a : probe ids to gene symbols
Tim Smith
- [BioC] chip-chip data
somnath bandyopadhyay
- [BioC] Protein Codes to Protein Names
Giulio Di Giovanni
- [BioC] KEGGgraph fails on a KEGG XML file
Rajarshi Guha
- [BioC] KEGGgraph fails on a KEGG XML file
Chris Fjell
- [BioC] IRanges RangedData - possible bug?
Janet Young
- [BioC] rtrackalyer too slow?
Wu, Xiwei
- [BioC] Loop design - biological, technical replication and contrasts
Gordon K Smyth
- [BioC] Cosmo background model
Prashantha Hebbar
- [BioC] Cosmo Background model
Prashantha Hebbar
- [BioC] Problem with xps package installation on Mac platform
steve shen
- [BioC] Problem with xps package installation on Mac platform
cstrato
- [BioC] Cosmo Background model
Prashantha Hebbar
- [BioC] Problem with xps package installation on Mac platform
cstrato
- [BioC] where to download 'probeset.cvs' file for creating scheme file
Steve Shen
- [BioC] chip-seq data analysis
Tiandao Li
- [BioC] Rintact equivalent in BioC2.6?
Fraser Sim
- [BioC] xps import data derived from different batches
Steve Shen
- [BioC] Loop design - biological, technical replication
Maciej Jończyk
- [BioC] regarding making of probe package
sneha patil
- [BioC] read.DNAStringSet
Ron Ophir
- [BioC] reverse engineering package
Weiwei Shi
- [BioC] Ensembl mart release 57: Useful information
Rhoda Kinsella
- [BioC] Call for papers: BCBGC-10, USA, July 2010
John Edward
- [BioC] Filter over group averages
Michael Imbeault
- [BioC] A question about org.Hs.egMAPCOUNTS
Hervé Pagès
- [BioC] question about forgeBSgenomeDataPkg function
Hervé Pagès
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] P-values to Z-scores
Paul Geeleher
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] March-April 2010*** R / S+ Essentials and Advanced Courses*** by XLSolutions Corp in San Francisco and other USA cities
sue at xlsolutions-corp.com
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] BioC 2.6 New Package Submission Deadline - 3/31/10
Patrick Aboyoun
- [BioC] intersection between genes and pathways
Alberto Goldoni
- [BioC] unable to load rtracklayer after install Iranges 1.5.56
sabrina s
- [BioC] clusterStab using a correlation distance
Daniel Brewer
- [BioC] can't use weights in single channel analysis?
Jenny Drnevich
- [BioC] fast iterator over DNAString's?
Paul Shannon
- [BioC] Reg: normalization of ArrayExpress data
Rohit Farmer
- [BioC] Reg: normalization of ArrayExpress data
Rohit Farmer
- [BioC] [MAANOVA] Warnings in fitmaanova & information request
Maciej Jończyk
- [BioC] Reg: normalization of ArrayExpress data
Rohit Farmer
- [BioC] Limma and logistic regression
Daniel Brewer
- [BioC] Limma-Contrasts-Question
Biju Joseph
- [BioC] Computational Biology Positions at EMBL (Heidelberg)
Wolfgang Huber
- [BioC] annotation in Ensembl using biomart
Jason Lu
- [BioC] pd.mapping250k.XXX & genome build GRCh37/hg19
Geoff Jentry
- [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan.
White, Peter
- [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan
White, Peter
- [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan
White, Peter
- [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan
White, Peter
- [BioC] (no subject)
Ana Staninska
- [BioC] limma: duplicate spots, technical replicates and biological replicates
Ana Staninska
- [BioC] color key - heatmap.2
Amit Indap
- [BioC] Limma-Contrasts-Question
Gordon K Smyth
- [BioC] [MAANOVA] Warnings in fitmaanova & information request
Maciej Jończyk
- [BioC] R/Maanova Tutorial
Ricardo Verdugo
- [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan
Gordon K Smyth
- [BioC] about formula in ancova
Dejian Zhao
- [BioC] silent data corruption in flowFlowJo, and fix
Hin-Tak Leung
- [BioC] about formula in ancova
Dejian Zhao
- [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow
Ivanek, Robert
- [BioC] a new bridge between bioperl and bioconductor
Zheng, Xin (NIH) [C]
- [BioC] extract intensity values from .cel using Affy probe ids
Rinku Saha
- [BioC] Problems installing Bioconductor Affy on Windows 7
Marissa LaMadrid
- [BioC] LIMMA Array Weight analysis
GAO Yu
- [BioC] AgiMicroRna package is not available at bioconductor or not in active form???
neeraj rana
- [BioC] questions regarding simpleaffy and justMAS
James Anderson
- [BioC] Reg: T-statistic using limma
Rohit Farmer
- [BioC] farms package fails on estrogen data
Javier Pérez Florido
- [BioC] affymetrix gene level arrays - cdf issue
Stefanie Tauber
- [BioC] Problems with Downloading packages
Abbhirami Rajagopal
- [BioC] rawQ Affymetrix
Dr Balazs Gyorffy
- [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Zhu, Julie
- [BioC] Ecoli antisense library
Balasubramanian Ganesan
- [BioC] log Fold Change
Jay
- [BioC] FW: Bioconductor
Dana.Stanley at csiro.au
- [BioC] (no subject)
Pete Shepard
- [BioC] AffyPLM's MAplot and cex
Timothy Wu
- [BioC] multicore package and AnnotationDbi
stephen.rudd at orionpharma.com
- [BioC] AgiMicroRna package is not available at bioconductor or not in active form???
Sean Davis
- [BioC] help on reading Agilent 44k 2 colour
Alberto Goldoni
- [BioC] problems when trying to use biomaRt
Juan Pablo Fededa
- [BioC] AgiMicroRna package is not available at bioconductor or not in active form???
Sean Davis
- [BioC] Fwd: problems when trying to use biomaRt
Sean Davis
- [BioC] problems when trying to use biomaRt
Juan Pablo Fededa
- [BioC] Package for Agilent microdata
Hersh
- [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes
Karl Brand
- [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes
Wolfgang Huber
- [BioC] getGEO - getting the .CEL files from GEO
張 語恬
- [BioC] limma lmFit error: Coefficients not estimable
Freydin, Maxim
- [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?
jeremy wilson
- [BioC] SNP plotter package
Kay Jaja
- [BioC] SPIA package
Marcos Pinho
- [BioC] Ecoli antisense library
James MacDonald
- [BioC] hclust for 13000 genes
avehna
- [BioC] CN analysis on a small Affymetrix GWS6 data set (Was: Re: QC Affy 6.0 SNP arrays with crlmm or Oligo?)
Henrik Bengtsson
- [BioC] Favor: ChIPpeakAnno
Zhu, Julie
- [BioC] calculating heterozygosity, and genetic diversity
Coghlan, Avril
- [BioC] MArray into data.frame for SPIA package
Marcos Pinho
- [BioC] IRanges: setting score() on RangedData drops rownames
Michael Dondrup
- [BioC] IRanges: cbind not well defined for RangedData?
Michael Dondrup
- [BioC] Tools for comparing microarray data on a snp level
Vincent Davis
- [BioC] microRNA: which genes code for a specific mirna?
Tim Smith
- [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth
Koen Marien
- [BioC] A statistical analyst or a post-doctoral position available immediately at Northwestern University
Pan Du
- [BioC] BiomaRt query
De Boever Patrick
- [BioC] Job: Bioinformatics Data Analyst in Vienna, Austria
Ido M. Tamir
- [BioC] GEOquery problem
Ding, Wei
- [BioC] xps: returns only 21 records
Steve Shen
- [BioC] request: calculate coverage with weight on RangedData object
Janet Young
- [BioC] MArray into data.frame for SPIA package
Gordon K Smyth
- [BioC] GO.db and org.XX.eg.db: update frequency?
Zhu, Julie
- [BioC] Get gene structure information: use biomaRt or other annotation packages?
Zhu, Julie
- [BioC] Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package
John Holden
- [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth
Koen Marien
- [BioC] xps: convert a data frame to ExprTreeSet
Steve Shen
- [BioC] ChIPpeakAnno get sequences from ranged data
Zhu, Julie
- [BioC] Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package
Gordon K Smyth
- [BioC] Beadarray data manipulation
Ramzi TEMANNI
- [BioC] function similar to phyper function that can handle 3 or more gene lists
Karl Brand
- [BioC] Question about iFlow
Abbhirami Rajagopal
- [BioC] a question related to nested R loop
aiguo li
- [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth
Audrey Kauffmann
- [BioC] Ecoli antisense library
James W. MacDonald
- [BioC] 64-bit R
Jin, Jp
- [BioC] Using RCurl to upload CEL files to a LIMS
stephen at mnemosyne.co.uk
- [BioC] Version package in release
Pierre-Yves
- [BioC] Agilent one colour
Yogi Sundaravadanam
- [BioC] Kmeans help
sidahmed BENABDERRAHMANE
- [BioC] GCRMA Normalization Differences between Windows and MAC
martin martinez
- [BioC] org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
Zhu, Julie
- [BioC] gene2pathway: Error in pathIDsLev1
Jean-Pierre DESVIGNES
- [BioC] limma lmFit error: Coefficients not estimable
Gordon K Smyth
- [BioC] Error: cannot allocate vector of size 13.7 Mb
neeraj rana
- [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems
Anthony Ferrari
- [BioC] how to do cross species annotation?
zrl
- [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems
Anthony Ferrari
- [BioC] Heatmap: row labels & dendogram
danieladna
- [BioC] where is the "getHomolog" function in biomaRt?
zrl
- [BioC] Not loading flowViz package
Sancho, Jose
- [BioC] building annotation package for porcine
Javier Pérez Florido
- [BioC] Call for papers (Deadline Extended): BCBGC-10, USA, July 2010
John Edward
- [BioC] GDD or alternative
Jonathan Arthur
- [BioC] Averaging duplicate probes in an RGList object
Tom Wenseleers
- [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?
Benoit Loup
- [BioC] regarding installaion of cdf package
sneha patil
- [BioC] error in limma read.images in linux ubuntu
Elmer Fernández
- [BioC] Gene IDs returned by RankProd topGene command
Blumenberg, Miroslav
- [BioC] IRanges: as.matrix.RangesMatching not found with NAMESPACE
Michael Dondrup
- [BioC] Question about plateCore
Abbhirami Rajagopal
- [BioC] [Bioc-sig-seq] ChIPpeakAnno get sequences from ranged data
Zhu, Julie
- [BioC] Limma: technical replicates in multi-group design
Adam Kiezun
- [BioC] silent data corruption in flowFlowJo, and fix
Gosink, John
- [BioC] Count differences between sequences
erikwright at comcast.net
- [BioC] Count differences between sequences
Patrick Aboyoun
- [BioC] GenomicFeatures question
Paul Leo
- [BioC] How to create a design matrix for a three-way design?
January Weiner
- [BioC] Error: could not find function "mixedModel2Fit"
neeraj rana
- [BioC] spillover method in flowCore package
Frederico Arnoldi
- [BioC] "mogene10stv1cdf"
Luqin Deng
- [BioC] error in limma read.images in linux ubuntu
Gordon K Smyth
- [BioC] Limma: technical replicates in multi-group design
Gordon K Smyth
- [BioC] Problem in running affy package
Priyanka Jain
- [BioC] Problem in running expresso command in affy package
Priyanka Jain
- [BioC] Svar: Bioconductor Digest, Vol 85, Issue 28
Vibe Henriette Skov
- [BioC] Count differences between sequences
erikwright at comcast.net
- [BioC] Spillover method in flowCore
Perry_D_Haaland at bd.com
- [BioC] Error in getCdfInfo(object)
Arun A K
- [BioC] KEGGgraph: retrieveKGML error (due to wrong ftp path)
Ludwig Geistlinger
- [BioC] error in gene2pathway results
Alberto Goldoni
- [BioC] checking multi-modalities in histograms
Javier Pérez Florido
- [BioC] filtering in GSEABase package
Jason Lu
- [BioC] readMicroRnaAFE function in AgiMicroR package
heyi xiao
- [BioC] stuck with affy/limma
Maxim
- [BioC] stuck with affy/ limma
Maxim
- [BioC] Error in getCdfInfo(object)
James MacDonald
- [BioC] [R] about the possible errors in Rgraphviz Package
HU,ZHENGJUN
- [BioC] [R] about the possible errors in Rgraphviz Package
HU,ZHENGJUN
- [BioC] Time-course microarray tutorial
Colin Gillespie
- [BioC] Clustering
Chintanu
- [BioC] Clustering
Chintanu
- [BioC] Accessing median and IQR values of MAplots
Javier Pérez Florido
- [BioC] simple functional analysis of gene lists
Rainer Tischler
- [BioC] question regarding qc function in simpleaffy package
James Anderson
- [BioC] removing probes from affybatch error
Jenny Drnevich
Last message date:
Wed Mar 31 23:37:22 CEST 2010
Archived on: Thu Apr 1 18:23:21 CEST 2010
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