January 2007 Archives by thread
Starting: Mon Jan 1 04:32:09 CET 2007
Ending: Wed Jan 31 23:38:52 CET 2007
Messages: 390
- [BioC] Plate or print-order effects - limma
Gordon Smyth
- [BioC] flagging spots in marray
Jay Konieczka
- [BioC] Import GEO Soft format
Daniel Brewer
- [BioC] Format identification
Daniel Brewer
- [BioC] flagging spots in marray
Gordon K Smyth
- [BioC] Modified qc.affy code for chip type: soybeancdf
Alvord, Greg (DMS) [Contr]
- [BioC] Limma: setting up printer information for agilent files
Daniel Brewer
- [BioC] .Rnw file
Lana Schaffer
- [BioC] post-doctoral fellowship in computational methods for systems genetics
Xinxia Peng
- [BioC] GOstats and custom annotation problem
Dario Greco
- [BioC] Limma: setting up printer information for agilent
Gordon K Smyth
- [BioC] Retrieve new informations for the probes used in th microarray!
Romain Desprat
- [BioC] beadarray: problem with reading in Bead Summary Data
P.D. Moerland
- [BioC] Converting an Annbuilder object to a dataframe
Daniel Brewer
- [BioC] cosmo package - Tk requirement?
Diggans, James C.
- [BioC] Oneclass SAM analysis
Brooke-Powell, Elizabeth
- [BioC] help with protein IPI annotation mappings
Kimpel, Mark William
- [BioC] How to include dye effect in the model for separate channel analysis of two-color Data using limma
Weiyin Zhou
- [BioC] warnings....when treating duplicates
Vinoy Kumar Ramachandran
- [BioC] marray, maSub, and image()
Jay Konieczka
- [BioC] normexp
Yolande Tra
- [BioC] matchrpobes and HGU95A mismatch
Bao Cao
- [BioC] read customized affymetrix chip
Bao Cao
- [BioC] Limma - background correction
João Fadista
- [BioC] simpleaffy and yeast2cdf problems
Dan Swan
- [BioC] Agilent 4100a probe annotation information
Daniel Brewer
- [BioC] Response - difference between hgu95aprobe and hgu95acdf
James W. MacDonald
- [BioC] Does anyone have a recent annotation for hgu133plus2 ??
Marco Zucchelli
- [BioC] hgu133plus2 updated annotation package
marco zucchelli
- [BioC] simpleaffy and yeast2cdf problems
Alvord, Greg (DMS) [Contr]
- [BioC] read.table(), then use affycoretools?
Weiyin Zhou
- [BioC] problem in biomaRt: getBM(output="list")
Georg Otto
- [BioC] read.table(), then use affycoretools?
Weiyin Zhou
- [BioC] read.table(), then use affycoretools?
Weiyin Zhou
- [BioC] typo in vennSelect help page
Kimpel, Mark William
- [BioC] making ExpressionSet from ArrayExpress
Wolfgang Huber
- [BioC] Problem with Rgraphviz on OSX with libgvc
Jarrett Byrnes
- [BioC] Memory issues with limma and ImaGen file import
CV Markus
- [BioC] Different RMA expression values in different BioC versions?
Quanli Wang
- [BioC] adding a color key scale to a DAG graph for Gene ontologies
marco zucchelli
- [BioC] adding a color key scale to a DAG graph for Gene ontologies
Li.Long at isb-sib.ch
- [BioC] gcrma with bpmap file instead of cdf file
Baoqiang Cao
- [BioC] continued dye effects, after normalization
Jenny Drnevich
- [BioC] limma - duplicateCorrelation
João Fadista
- [BioC] snapCGH - processCGH
João Fadista
- [BioC] goTools problem
Jorrit Boekel
- [BioC] ABPkgBuilder error: unable to find an inherited method for function "baseFile<-"
Martin Kircher
- [BioC] Arabidopsis tiling arrays
Liam Childs
- [BioC] hist: log Intensity
Mohammad Esad-Djou
- [BioC] split-plot factorial design with limma?
Valeria Edefonti
- [BioC] which universe in hyperGTest
marco zucchelli
- [BioC] limma - reading data from different Print files in cDNA
Dipen Sangurdekar
- [BioC] gcrma with bpmap file instead of cdf file
Baoqiang Cao
- [BioC] which universe in hyperGTest
marco zucchelli
- [BioC] simpleaffy segmentation fault
Sucheta Tripathy
- [BioC] gcrma with bpmap file instead of cdf file
Baoqiang Cao
- [BioC] Bioinformatician/Ontologist position in the Microarray Team at the EBI.
aedin culhane
- [BioC] hyperG over chromosome position...?
Dario Greco
- [BioC] Delivery Status Notification (Failure)
Dr. D. P. Kreil (Boku)
- [BioC] Affymetrix Tiling Arrays and TilingArray package
joseph
- [BioC] mergeLevels (aCGH) vs. MergeLevels.new
Ramon Diaz-Uriarte
- [BioC] Problem using biomaRt with local database
Alessandro Bruselles
- [BioC] ABPkgBuilder error: unable to find an inherited method for function "baseFile<-"
John Zhang
- [BioC] 2x2 factorial with dye effect, limma design
Gordon K Smyth
- [BioC] removing outlier/masked probes and gcrma
Andrew Su
- [BioC] continued dye effects, after normalization
Gordon Smyth
- [BioC] problems reading Illumina files using BeadExplorer
Sylvain.Pradervand
- [BioC] Advanced Course in Cambridge 30.3.+1.4.
Wolfgang Huber
- [BioC] outdated version of 'affy' in biocLite ?
Talloen, Willem [PRDBE]
- [BioC] Rgraphviz installation mac os x intel
Gavai, Anand
- [BioC] removing outlier/masked probes and gcrma
Andrew Su
- [BioC] MANOR/GLAD, problems getting data into the arrayCGH object
James Morris
- [BioC] [Bioc] Removing outlier/masked probes and gcRMA
Amy Mikhail
- [BioC] "oligo" crashes in windows XP
Morten Mattingsdal
- [BioC] Error of pamr.knnimpute
washiot+1 at gmail.com
- [BioC] saturated spots
Hans-Ulrich Klein
- [BioC] Limma - error when using duplicateCorrelation - Windows ver. Linux
Jakob Hedegaard
- [BioC] Nimbleexpress arrays
Saroj Mohapatra
- [BioC] Problems with the size of the plots obtained with AffyPLM
Jordi Altirriba Gutiérrez
- [BioC] suggestions for plotPCA / pca.legend
Jenny Drnevich
- [BioC] AnnBuilders paseData() doesn't recognize ACCs with underscore?
Benjamin Otto
- [BioC] Using ontoCompare with local GO database
Alessandro Bruselles
- [BioC] AnnBuilders paseData() doesn't recognize ACCs with underscore?
John Zhang
- [BioC] questions on BioC's implementation of plier
Jenny Drnevich
- [BioC] data set validation
Lana Schaffer
- [BioC] nested design in limma? -- revisit
Shi, Tao
- [BioC] imputing missing data for 70mer array platform, need advice
Betty Gilbert
- [BioC] Limma - error when using duplicateCorrelation - Windows ver. Linux
Gordon Smyth
- [BioC] Postions Available at Tufts Universtiy, Boston.
Lakshmanan Iyer
- [BioC] from BAC name to list of genes in that BAC
Federico Abascal
- [BioC] AnnBuilders paseData() doesn't recognize ACCs with underscore?
John Zhang
- [BioC] Quality Assessment
Lana Schaffer
- [BioC] using simpleaffy incorrectly, or is there a problem with the read.affy function?
k. brand
- [BioC] imputing missing data for 70mer array platform, need advice
Sean Davis
- [BioC] Rgraphviz problem
Marcelo Laia
- [BioC] hyperGTest on proteomics data
Kimpel, Mark William
- [BioC] make.cdf.package
Lana Schaffer
- [BioC] Annals of Applied Statistics
Michael Newton
- [BioC] Time course cDNA two color array analysis
Marcelo Laia
- [BioC] R/Bioconductor Wrappers for NCBI eUtils (Entrez Programming Utilities)?
Earl F. Glynn
- [BioC] blast
Jay Konieczka
- [BioC] cghMCR bug?
Ramon Diaz-Uriarte
- [BioC] cghMCR bug?
John Zhang
- [BioC] about gene annotation
yanju
- [BioC] statistical analyst
Wang, Hui
- [BioC] Newbie needs help with exprset
Sarah Highlander
- [BioC] Mouse.lumi problems
Anand C. Patel
- [BioC] Reading hundrets of .cel files and QC thereof
Wolfgang Raffelsberger
- [BioC] Newbie needs help with exprset
Naomi Altman
- [BioC] warnings when using liwong summary method in affy
marco zucchelli
- [BioC] Normallization for focused chips
Lana Schaffer
- [BioC] DSC 2007 Additional Funding
Paul Murrell
- [BioC] what is the equivalent of normalize.qspline for 2 color arrays?
Betty Gilbert
- [BioC] memory problem
yoo hoo
- [BioC] Reading hundrets of .cel files and QC thereof
Aedin Culhane
- [BioC] Advice on how to compare two different sources on cDNA
Marcelo Laia
- [BioC] help in normalization cDNA arrays
Marcelo Laia
- [BioC] How do you sort the differentially expressed genes?
De-Jian ZHAO
- [BioC] [limma] Error: nestedF method can't handle NA p-values
Marcelo Laia
- [BioC] limma vs. maanova for expirement with both contrasts and continuous variables
Kimpel, Mark William
- [BioC] job - computational biology position at Vertex Pharmaceuticals, Boston
Brian Hare
- [BioC] Normallization for focused chips
Gordon K Smyth
- [BioC] tiling array normalization
Lana Schaffer
- [BioC] Results file LIMMA
Andres Gutierrez
- [BioC] Spot duplicate in timecourse package and "missing" values
Marcelo Laia
- [BioC] limma vs. maanova for expirement with both contrasts and continuous variables
Gordon Smyth
- [BioC] Time course cDNA two color array analysis
Marcelo Laia
- [BioC] Normallization for focused chips
martin.schumacher at novartis.com
- [BioC] localization of mm values in affybatch exprs matrix
Karin Lagesen
- [BioC] problems with library goCluster
Caroline Reiff
- [BioC] warnings from li wong summary method in expresso
marco zucchelli
- [BioC] R fonts: character set (male/female symbols)
J.delasHeras at ed.ac.uk
- [BioC] downloading GEO gds files
Wall, Dennis Paul
- [BioC] Differentially Expressed Genes in Time Series with Replications
Peter Robinson
- [BioC] GOstats hyperGTest question
ivan.borozan at utoronto.ca
- [BioC] [limma] Error: nestedF method can't handle NA p-values
Gordon K Smyth
- [BioC] Results file LIMMA
Gordon K Smyth
- [BioC] Pathway Interaction Database with BioC?
A.J. Rossini
- [BioC] problem with biomaRt getHomolog function
Kimpel, Mark William
- [BioC] how do you make a decoding dataframe affy2locusDF
Caroline Reiff
- [BioC] Loading multiple Affy chips simultaneously
Paul Boutros
- [BioC] Loading multiple Affy chips simultaneously
Paul Boutros
- [BioC] (no subject)
Qing Jing
- [BioC] [COURSE ANNOUNCEMENT] CSAMA'07
stefano iacus
- [BioC] Announcement: BioConductor Developer Workshop
Darlene Goldstein
- [BioC] Rgraphviz on Fedora Core 6
Byron Wallace
- [BioC] gcrma and chip without mm values
Karin Lagesen
- [BioC] Latest Stable Limma Version
Alejandro
- [BioC] Ensuring two graphs have the same layout in Rgraphviz
michael watson (IAH-C)
- [BioC] Fwd: Ensuring two graphs have the same layout in Rgraphviz
Tony Chiang
- [BioC] Ensuring two graphs have the same layout in Rgraphviz
Tony Chiang
- [BioC] Bioconductor Digest, Vol 47, Issue 26
Manhong Dai
- [BioC] Looking for R package for Nimblegen expression data
Xinxia Peng
- [BioC] Looking for R package for Nimblegen expression data
Xinxia Peng
- [BioC] Looking for R package for Nimblegen expression data
Xinxia Peng
- [BioC] aCGH.process help
Lee, Jason Thanh
- [BioC] reposTools
Qing Jing
- [BioC] Rgraphviz on Fedora Core 6
Li.Long at isb-sib.ch
- [BioC] Latest Stable Limma Version
Gordon K Smyth
- [BioC] Analysis with MBNI re-mapped (custom) CDF files
Hooiveld, Guido
- [BioC] AnnBuilder
Qing Jing
- [BioC] rcor.test
Damion Colin Nero
- [BioC] meaning of pfp in RankProd
Matthew McCormack
- [BioC] annotation packages version/date for sources
Ido M. Tamir
- [BioC] annaffy errors
Ido M. Tamir
- [BioC] aCGH data format
Lee, Jason Thanh
- [BioC] dChip v li.wong() (Was: Re: warnings from li wong summary method in expresso)
Henrik Bengtsson
- [BioC] possible spam alert
Kimpel, Mark William
Last message date:
Wed Jan 31 23:38:52 CET 2007
Archived on: Fri Feb 2 19:14:12 CET 2007
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