February 2006 Archives by thread
Starting: Wed Feb 1 00:01:25 CEST 2006
Ending: Tue Feb 28 23:11:41 CEST 2006
Messages: 366
- [BioC] weights & normalizeBetweenArrays
Gordon Smyth
- [BioC] affy: How to back transform the matrix to a vector? (low-level imaging)
Simon Lin
- [BioC] ad hoc tools for affy tiling arrays?
Kasper Daniel Hansen
- [BioC] Graph Layout
Li Long
- [BioC] ad hoc tools for affy tiling arrays?
Dario Greco
- [BioC] microarray database
Thomas Litman
- [BioC] heatmap
kfbargad at ehu.es
- [BioC] limma design: a basics questions for factorial analysis
Marcelo Luiz de Laia
- [BioC] widgetTools wFuns problem
mattia
- [BioC] error in limma read.maimages(files, source="imagene")
Georg Otto
- [BioC] Request for users of limmaGUI, affylmGUI, JSM2005 or IBC2004 microarray course websites or my R-Tcl/Tk examples
James Wettenhall
- [BioC] problems with GO package data
Yu-An Dong
- [BioC] RMA - answer found- AND ANOTHER QUESTION
Richard Friedman
- [BioC] Drawing network graphs (i.e. nodes and edges)
Peter
- [BioC] Annotation packages for E.Coli
Alex Sanchez
- [BioC] how to add contrast for lmFit in limma?
Jianping Jin
- [BioC] getBioC problem
Amy Mikhail
- [BioC] design matrix question
Marcelo Luiz de Laia
- [BioC] Hier.Clustering: group size effect
Heike Pospisil
- [BioC] error in limma read.maimages(files, source="imagene")
Gordon K Smyth
- [BioC] widgetTools wFuns problem
John Zhang
- [BioC] mapping probes between different platforms
Mattias de Hollander
- [BioC] mapping probes between different platforms [again]
Mattias de Hollander
- [BioC] mouse 430_2 error message
Dmitry
- [BioC] annotation hgu133plus2 problem,
Saurin D. Jani
- [BioC] affy chips' quality control question
Na, Ren
- [BioC] Workshop : Statistical Analysis of Genetic and Gene Expression Data
Adaikalavan Ramasamy
- [BioC] justRMA using incorrect default cdf
Kimpel, Mark William
- [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error
Henrik Hornshøj Jensen
- [BioC] [RClassification on Imbalanced Data
portnoy at supereva.it
- [BioC] Calculating the average differential exprression
michael watson (IAH-C)
- [BioC] getBioC problem
Gaj Stan (BIGCAT)
- [BioC] getBioC problem
Gaj Stan (BIGCAT)
- [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error
John Zhang
- [BioC] Job Posting: "Lab head Biomarker"
Michael Seewald
- [BioC] justRMA using incorrect default cdf
Kimpel, Mark William
- [BioC] M vs M plots- dye effect in dyeswap exp
lzarzabal at aol.com
- [BioC] [Fwd: Fwd: M vs M plots- dye effect in dyeswap exp]
zarzabal
- [BioC] biocLite.R
Glazko, Galina
- [BioC] heatmap
kfbargad at ehu.es
- [BioC] diagnostics
alex lam (RI)
- [BioC] bioconductor.org downloads available again
Seth Falcon
- [BioC] affy chips' quality control question
Na, Ren
- [BioC] problems with hgu133a2?
Dick Beyer
- [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error
Henrik Hornshøj Jensen
- [BioC] topTable output ptoblem
Assa Yeroslaviz
- [BioC] topTable output ptoblem
Stephen Henderson
- [BioC] getBioC problem
Amy Mikhail
- [BioC] info su illumina
Alberto Goldoni
- [BioC] limma anova table?
Jianping Jin
- [BioC] continued problems with ReadAffy
Kimpel, Mark William
- [BioC] info su illumina
Oosting, J. (PATH)
- [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error
Henrik Hornshøj Jensen
- [BioC] info su illumina
Sean Davis
- [BioC] plier 1.2.0 compilation error (FC4 64bits)
Ariel Chernomoretz
- [BioC] problems using getGEO
Juan Rodriguez
- [BioC] GCRMA explained in words
Richard Friedman
- [BioC] Bioconductor installation problem
caiwei at mdanderson.org
- [BioC] continued problems with ReadAffy
Kimpel, Mark William
- [BioC] info su illumina
Rahman, Fatimah
- [BioC] diagnostics
alex lam (RI)
- [BioC] info su illumina
Lynn Amon
- [BioC] Fetching documents from PubMed
Kaustubh Patil
- [BioC] Help downloading limma into R
Michael Stapelberg
- [BioC] Limma: Amean problem
david hot
- [BioC] GCRMA and background
Amy Mikhail
- [BioC] how to evaluate an Affymetrix custom sequencing chip
Dr_Gyorffy_Balazs
- [BioC] justGCRMA memory problem
Jianping Jin
- [BioC] CATMA Metadata
Johannes Hanson
- [BioC] affy scalevalue for RMA?
Celine Carret
- [BioC] Description of affy paper by Gautier, Irizarry, Cope and Bolstad, 2005
Alvord, Greg (DMS) [Contr]
- [BioC] passing arguments to makeContrast
rcaloger
- [BioC] limma question
Michael Stapelberg
- [BioC] Limma question
alex lam (RI)
- [BioC] Siggenes problem with sam.snp()
Vincent Negre
- [BioC] Genomic DNA as a reference and limma
john seers (IFR)
- [BioC] Genomic DNA as a reference and limma
michael watson (IAH-C)
- [BioC] Timeseries loop design analysis using Limma or Maanova?
Pete
- [BioC] ANN: Introductory R and Bioconductor Mini Course , Seattle, April 12-14
Nianhua Li
- [BioC] GEOquery & GDS2eSet error
Morten Mattingsdal
- [BioC] RMA normalization when using subsets of samples
Sylvia.Merk at ukmuenster.de
- [BioC] interpretation of vsn normalized data
Maurice Melancon
- [BioC] RMA normalization when using subsets of samples
martin.schumacher at novartis.com
- [BioC] Affy Package - MAplot Function help needed...
Joern Wessels
- [BioC] RMA normalization when using subsets of samples
Ron Ophir
- [BioC] LPE
Nicolas Servant
- [BioC] interpretation of vsn normalized data
Maurice Melancon
- [BioC] ANN: BioC2006 Conference Scheduled for August in Seattle
Nianhua Li
- [BioC] comparing correlation coefficients
Ilhem Diboun
- [BioC] Run GOHyperG without specifying a chip
knaxerov at ix.urz.uni-heidelberg.de
- [BioC] Data Frame Error in Affycomp
John.Brozek at it-omics.com
- [BioC] Differences: mas5/mas5calls vs. call.expr/pairwise.comparison
Benjamin Otto
- [BioC] comparing correlation coefficients (fwd)
Ilhem Diboun
- [BioC] GeneR
Antoine Lucas
- [BioC] Question: limma decideTests nestedF p-values
Georg Otto
- [BioC] LPE question
Jain, Nitin
- [BioC] problem to compare two series of arrays hybridized with two different protocols
Malick.PAYE at eu.biomerieux.com
- [BioC] Inherits(x,"data.frame") error in SamR
McGee, Monnie
- [BioC] SNPgenotyping
Justin Borevitz
- [BioC] Inherits(x,"data.frame") error in SamR
McGee, Monnie
- [BioC] Trouble building Bioconductor
Atro Tossavainen
- [BioC] Confusion over limma documentation and design/contrast matrix
Assa Yeroslaviz
- [BioC] Fwd: Re: Run GOHyperG without specifying a chip
Mikko Arvas
- [BioC] problem to compare two series of arrays hybridized with two different protocols
Stephen Henderson
- [BioC] Confusion over limma documentation and design/contrast matrix
Assa Yeroslaviz
- [BioC] normalization of duplicate spots
Jianping Jin
- [BioC] extract lmFit results?
Jianping Jin
- [BioC] Invalid fold-filter
Bornman, Daniel M
- [BioC] Invalid fold-filter
Bornman, Daniel M
- [BioC] Geneplotter (won't) Makesense - help please
Quentin Anstee
- [BioC] Invalid fold-filter
Wittner, Ben, Ph.D.
- [BioC] reporterInfo for exprSet subsets
Christos Hatzis
- [BioC] reporterInfo for exprSet subsets
Christos Hatzis
- [BioC] clustering question
Kimpel, Mark William
- [BioC] extracting probe sets corresponding to a given gene
Christos Hatzis
- [BioC] probe level summarization before classification
Talloen, Willem [PRDBE]
- [BioC] Limma: bad spots flagged out?
Ana Conesa
- [BioC] Invalid fold-filter
Bornman, Daniel M
- [BioC] question about pm() and order of probes returned
Jason Affourtit
- [BioC] background correction
Pedro López Romero
- [BioC] clustering question
Kimpel, Mark William
- [BioC] Invalid fold-filter
Stephen Henderson
- [BioC] extracting probe sets corresponding to a given gene
Christos Hatzis
- [BioC] Annotation and gene ontology for a mosquito array
Amy Mikhail
- [BioC] nested design in limma?
Jenny Drnevich
- [BioC] missing probeids in mu11ksuba metadata
Dick Beyer
- [BioC] limma anova table?
Gordon K Smyth
- [BioC] Limma missing values
Gordon K Smyth
- [BioC] Question: limma decideTests nestedF p-values
Gordon K Smyth
- [BioC] Limma: bad spots flagged out?
Gordon K Smyth
- [BioC] List significant genes on a GO table
Quentin Anstee
- [BioC] reporterInfo for exprSet subsets
Christos Hatzis
- [BioC] Recall: reporterInfo for exprSet subsets
Christos Hatzis
- [BioC] reporterInfo for exprSet subsets
Christos Hatzis
- [BioC] biomaRt xMLTreeParse error
Matt Ritchie
- [BioC] probe level summarization before classification
Naomi Altman
- [BioC] advice on Biostrings
Rafael A Irizarry
- [BioC] nimblegen ChIP to chip array
ping_zheng at mail.wsu.edu
- [BioC] nimblegen ChIP to chip array
ping zheng
- [BioC] Problem with A mean in Limma
david hot
- [BioC] install package from local path with reposTools
Axel Rasche
- [BioC] RMySQL
Amy Mikhail
- [BioC] Getting MeSH
Kaustubh Patil
- [BioC] coerce aafTable object into dataframe (annaffy)
Georg Otto
- [BioC] Fetching documents from PubMed
Kaustubh Patil
- [BioC] limma question
Sun, Yezhou
- [BioC] nested design in limma?
STKH (Steen Krogsgaard)
- [BioC] AnnBuilder built package not supported in R 2.2.0
Brian Parker
- [BioC] RNA degradation tends & options for analysis
Juanma Vaquerizas
- [BioC] Filter on Fold Change
Quentin Anstee
- [BioC] Filter on Fold Change
Stephen Henderson
- [BioC] AnnBuilder built package not supported in R 2.2.0
John Zhang
- [BioC] duplicate cor?
Jianping Jin
- [BioC] clustering question
Kimpel, Mark William
- [BioC] limma question
James W. MacDonald
- [BioC] Problem with A mean in Limma
Gordon Smyth
- [BioC] plotting sam results in one window
Assa Yeroslaviz
- [BioC] BioC Developers Meeting
Wolfgang Huber
- [BioC] limma,weights & fit
daniela marconi
- [BioC] Problems annotating a gene list
Quentin Anstee
- [BioC] limma question
Sun, Yezhou
- [BioC] limma question
James W. MacDonald
- [BioC] AnnBuilder error
Aedin Culhane
- [BioC] coerce aafTable object into dataframe (annaffy)
Colin A. Smith
- [BioC] BioC] limma question
Gordon Smyth
- [BioC] Explaining limma, design matrices and linear models to non statisticians
michael watson (IAH-C)
- [BioC] Limma: can't use plotPrintTipLoess() with split.screen()
michael watson (IAH-C)
- [BioC] problems with read.marrayRaw
Jenny Russ
- [BioC] makePlatformDesign for 10k Array
Tim Strom
- [BioC] Normalizing by Within Condition - a bad idea
Naomi Altman
- [BioC] Limma and time-course data
michael watson (IAH-C)
- [BioC] Another question about dye swap
Ron Ophir
- [BioC] (no subject)
Alessandra De Riva
- [BioC] Limma and time-course data
michael watson (IAH-C)
- [BioC] Sales
Rafael A Irizarry
- [BioC] Sales
Paul Grosu
- [BioC] LIMMA help: how to choose correct weight for flagged spots??
daniela marconi
- [BioC] Trouble building Bioconductor
Herve Pages
- [BioC] Trouble building Bioconductor
Atro Tossavainen
- [BioC] degraded RNA and background correction
Jenny Drnevich
- [BioC] All the functions in a BioC package
Khan, Sohail
Last message date:
Tue Feb 28 23:11:41 CEST 2006
Archived on: Wed Mar 1 21:47:27 CEST 2006
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