September 2004 Archives by subject
Starting: Wed Sep 1 02:33:26 CEST 2004
Ending: Thu Sep 30 19:54:11 CEST 2004
Messages: 296
- [BioC] (no subject)
Paul Boutros
- [BioC] [Fwd: Re: using gcrma in expresso]
echang4 at life.uiuc.edu
- [BioC] A question about MAS5 vs RMA vs GCRMA
YUK FAI LEUNG
- [BioC] A question about MAS5 vs RMA vs GCRMA
Adaikalavan Ramasamy
- [BioC] A question about MAS5 vs RMA vs GCRMA
Martino Barenco
- [BioC] A question about MAS5 vs RMA vs GCRMA
YUK FAI LEUNG
- [BioC] about siggenes
haojie
- [BioC] about siggenes
Robert Gentleman
- [BioC] about siggenes
Holger Schwender
- [BioC] about siggenes
haojie
- [BioC] Advice on print-tip normalization
Gene Cutler
- [BioC] affy and limma
Gareth Elvidge
- [BioC] Affy empty line
Hee Siew Wan
- [BioC] Affymetrix is changing its labelling kit - data
analysiswill change!?
Francois Collin
- [BioC] Affymetrix is changing its labelling kit - data analysis
will change!?
Matthew Hannah
- [BioC] Affymetrix P calls
Stephen Henderson
- [BioC] Affymetrix P calls
Susmita Datta
- [BioC] AnnBuilder
Catalin Barbacioru
- [BioC] AnnBuilder
Robert Gentleman
- [BioC] AnnBuilder/ABPkgBuilder: lots of Errors
Floor Stam
- [BioC] AnnBuilder/ABPkgBuilder: lots of Errors
John Zhang
- [BioC] AnnBuilder/ABPkgBuilder: lots of Errors
Floor Stam
- [BioC] AnnBuilder/ABPkgBuilder: lots of Errors
John Zhang
- [BioC] Application of PAMR from Affy to spot data
Tan, MinHan
- [BioC] Application of PAMR from Affy to spot data
Robert Gentleman
- [BioC] averaging expression values in limma
Ana Conesa
- [BioC] Bad Data Sets needed!
michael watson (IAH-C)
- [BioC] Bioconductor release 1.5 notes
Jeff Gentry
- [BioC] bug in reposTools 1.4.11: missing getRversion
Jeff Gentry
- [BioC] bug in reposTools 1.4.11: missing getRversion
Ivo Kwee
- [BioC] Calculating microarray ratios between channels from
different arrays
michael watson (IAH-C)
- [BioC] Common reference design and intercept in limma
Sean Davis
- [BioC] Common reference design and intercept in limma
Gordon K Smyth
- [BioC] contrasts.fit Error
Matt McCall
- [BioC] contrasts.fit Error
Gordon K Smyth
- [BioC] contrasts.fit Error
Matt McCall
- [BioC] contrasts.fit Error
Gordon K Smyth
- [BioC] Correct use of a distance measure when clustering gene
expression data
michael watson (IAH-C)
- [BioC] Correct use of a distance measure when clustering gene
expression data
Floor Stam
- [BioC] Creating a substet of probe intensities from AffyBatch
object
Larry.Lapointe at csiro.au
- [BioC] Creating a substet of probe intensities from AffyBatch
object
Laurent Gautier
- [BioC] Creating a substet of probe intensities from AffyBatch object
Larry La Pointe
- [BioC] dChip
Lizhe Xu
- [BioC] dChip
Ben Bolstad
- [BioC] Do I now understand Limma contrast matrices??
Matthew Hannah
- [BioC] Error getting packages from repository
Sean Davis
- [BioC] Error getting packages from repository
Jeff Gentry
- [BioC] Error getting packages from repository
Sean Davis
- [BioC] Error in kooperberg procedure
michael watson (IAH-C)
- [BioC] Error in kooperberg procedure
Matthew Ritchie
- [BioC] Error with library(limma) with R2.0 devel
Matthew Hannah
- [BioC] Error with library(limma) with R2.0 devel
Gordon Smyth
- [BioC] Error with library(limma) with R2.0 devel
Jeff Gentry
- [BioC] Error with library(limma) with R2.0 devel
Matthew Hannah
- [BioC] Error with library(limma) with R2.0 devel
James W. MacDonald
- [BioC] error with update.package2
Adaikalavan Ramasamy
- [BioC] error with update.package2
Adaikalavan Ramasamy
- [BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel
Matthew Hannah
- [BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel
Matthew Hannah
- [BioC] Errors with -Inf
michael watson (IAH-C)
- [BioC] excluding absent genes - again
Arne.Muller at aventis.com
- [BioC] Expression levels in GCRMA and MAS5.0 and cut-off
Jordi Altirriba Gutiérrez
- [BioC] Expression levels in GCRMA and MAS5.0 and cut-off
Zhijin Wu
- [BioC] Expression levels in GCRMA and MAS5.0 and cut-off
Jordi Altirriba Gutiérrez
- [BioC] Extracting normalized intensities
Gene Cutler
- [BioC] Extracting normalized intensities
Jean Yee Hwa Yang
- [BioC] fibroblasts and endothelial cells
Ulrich Pfeffer
- [BioC] fibroblasts and endothelial cells
Phguardiol at aol.com
- [BioC] Finding and controlling for dye bias in Limma
Sean Davis
- [BioC] Finding and controlling for dye bias in Limma
Gordon K Smyth
- [BioC] Friedman test
Arne.Muller at aventis.com
- [BioC] function pubmed and large requests
Kimpel, Mark W
- [BioC] gcrma background
Ariel Chernomoretz
- [BioC] gcrma background
Zhijin Wu
- [BioC] GCRMA publication
Margaret Gardiner-Garden
- [BioC] GCRMA publication
Steffen Durinck
- [BioC] GCRMA publication
Zhijin Wu
- [BioC] GCRMA/RMA bimodal distribution
Matthew Hannah
- [BioC] HGU95A and HGU95ACDF
S Peri
- [BioC] HGU95A and HGU95ACDF
John Zhang
- [BioC] high poportion of identical expression measure with RMA
and 3 arrays (addendum)
Adaikalavan Ramasamy
- [BioC] high poportion of identical expression measure with RMA and 3
arrays
Adaikalavan Ramasamy
- [BioC] How do I make exprSet?
Hao Liu
- [BioC] How do I make exprSet?
Robert Gentleman
- [BioC] how to do MAS background correction for Mismatch?
F Duan
- [BioC] how to do MAS background correction for Mismatch?
James W. MacDonald
- [BioC] how to do MAS background correction for Mismatch?
F Duan
- [BioC] How to get gene names in arabidopsis arrays
Fangxin Hong
- [BioC] How to get gene names in arabidopsis arrays
Robert Gentleman
- [BioC] How to save image to JPEG version under Linux?
F Duan
- [BioC] How to save image to JPEG version under Linux?
Zhijin Wu
- [BioC] How to save image to JPEG version under Linux?
Sean Davis
- [BioC] IBM developerworks article on R (intro, part 1)
Paul Grosu
- [BioC] identify gene expression markers using Bayesian
Liu, Xin
- [BioC] Install HGU133a_tag in Linux.
Lei Zhou
- [BioC] Install HGU133a_tag in Linux.
Jeff Gentry
- [BioC] Is it right?
Kaushik, Narendra K
- [BioC] Is it right?
michael watson (IAH-C)
- [BioC] Is it right?
Caimiao Wei
- [BioC] Kooperberg
Jason Skelton
- [BioC] Kooperberg
Matthew Ritchie
- [BioC] latest devel GO package not built in R2.0.0
Dick Beyer
- [BioC] latest devel GO package not built in R2.0.0
John Zhang
- [BioC] latest devel GO package not built in R2.0.0
Dick Beyer
- [BioC] latest devel GO package not built in R2.0.0
John Zhang
- [BioC] Li Wong PM-only "background" correction
Ann Hess
- [BioC] Li Wong PM-only "background" correction
Laurent Gautier
- [BioC] limma & targets
Giovanni Coppola
- [BioC] limma & targets
Gordon Smyth
- [BioC] limma Dye Swap question
Mike Schaffer
- [BioC] limma Dye Swap question
Ramon Diaz-Uriarte
- [BioC] limma moderated t-statistics and B-statistics
Gordon Smyth
- [BioC] LimmaGUI Background corrections
Elizabeth Brooke-Powell
- [BioC] Loading gal files with marray
Daniel Iordan
- [BioC] Loading gal files with marray
Daniel Iordan
- [BioC] Loess normalization for Agilent chips
Malard, Joel M
- [BioC] Loess normalization for Agilent chips
A.J. Rossini
- [BioC] Loess normalization for Agilent chips
Malard, Joel M
- [BioC] MAS problem
Michael Barnes
- [BioC] MAS problem
Adaikalavan Ramasamy
- [BioC] MAS, RMA or DChip. Which is better?
narinder.singh
- [BioC] MAS5 and GCOC difference to get CEL files
Delphine Fleury
- [BioC] MAS5 and GCOC difference to get CEL files
Adaikalavan Ramasamy
- [BioC] MAS5 and GCOC difference to get CEL files
James W. MacDonald
- [BioC] MAS5 and GCOC difference to get CEL files
Adaikalavan Ramasamy
- [BioC] MAS5 and GCOC difference to get CEL files
Remo Sanges
- [BioC] MAS5 and GCOC difference to get CEL files
Matthew Hannah
- [BioC] mas5calls error with YG_S98 CEL files
Bruz Marzolf
- [BioC] mas5calls error with YG_S98 CEL files
Bruz Marzolf
- [BioC] mas5calls error with YG_S98 CEL files
Crispin Miller
- [BioC] matchprobes for GCRMA
Victoria Perreau
- [BioC] matchprobes for GCRMA
Adaikalavan Ramasamy
- [BioC] memory management in Win XP
Kimpel, Mark W
- [BioC] memory management in Win XP
Robert Gentleman
- [BioC] Metadata for Atgenome1 array
andy phillips (RRes-Roth)
- [BioC] Metamorph
E Motakis, Mathematics
- [BioC] missing xy2i and i2xy functions
Nisha Mulakken
- [BioC] missing xy2i and i2xy functions
James MacDonald
- [BioC] Modelling interaction using limma package
Ramon Diaz-Uriarte
- [BioC] Modelling interaction using limma package
Fangxin Hong
- [BioC] Modelling interaction using limma package
Ramon Diaz-Uriarte
- [BioC] Modelling interaction using limma package
Fangxin Hong
- [BioC] Normalisation of focussed arrays and Taq-man gene cards
Aedin
- [BioC] Normalising divergent samples.
Matthew Hannah
- [BioC] Normalising divergent samples.
Arne.Muller at aventis.com
- [BioC] normalize.invariantset
cchetia at vbi.vt.edu
- [BioC] normalize.invariantset
cchetia at vbi.vt.edu
- [BioC] number of grid columns is not 4 - error
Morten
- [BioC] number of grid columns is not 4 - error
Gordon K Smyth
- [BioC] odd results from vennCounts()
Jacqueline Hall
- [BioC] odd results from vennCounts()
Gordon Smyth
- [BioC] odd results from vennCounts()
Gordon Smyth
- [BioC] Package for ArrayWoRx output-files
Kim Holmstrøm
- [BioC] package mgu74av2 version 2.0.0 install
Florence Combes
- [BioC] package mgu74av2 version 2.0.0 install
John Zhang
- [BioC] package mgu74av2 version 2.0.0 install
Florence Combes
- [BioC] package mgu74av2 version 2.0.0 install
Jeff Gentry
- [BioC] package mgu74av2 version 2.0.0 install
Florence Combes
- [BioC] package Ruuid
alberto goldoni
- [BioC] package Ruuid
Robert Gentleman
- [BioC] package Ruuid
alberto goldoni
- [BioC] package Ruuid
Douglas Bates
- [BioC] plot.ProbeSet
Peter Lee
- [BioC] Problem with BioC
Kaushik, Narendra K
- [BioC] Problem with BioC
Robert Gentleman
- [BioC] Problem with BioC
James MacDonald
- [BioC] Problem with BioC
Jeff Gentry
- [BioC] Problem with gls.series in limma
Fangxin Hong
- [BioC] Problem with gls.series in limma
Gordon Smyth
- [BioC] Problems with BioConductor
Alexandra-mariela Dumitru
- [BioC] Problems with BioConductor
Jeff Gentry
- [BioC] Question
Sandya Liyanarachchi
- [BioC] Question
alberto goldoni
- [BioC] question about distribution
Phguardiol at aol.com
- [BioC] questions about U133A cdf packages
Wenlei Liu
- [BioC] questions about U133A cdf packages
James W. MacDonald
- [BioC] r devel ????
Alberto Goldoni
- [BioC] r devel ????
James W. MacDonald
- [BioC] r devel ????
Kasper Daniel Hansen
- [BioC] r devel ????
Jeff Gentry
- [BioC] RBGL 1.2.2 compilation problem
Roels, Steven
- [BioC] Re: [R] unable to download
Jeff Gentry
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] Re: [S] Error in clustering procedure
James W. MacDonald
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] Re: [S] Error in clustering procedure
David K Pritchard
- [BioC] Re: [S] Error in clustering procedure
Ramon Diaz-Uriarte
- [BioC] Re: [S] Error in clustering procedure
Prof Brian Ripley
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] Re: [S] Error in clustering procedure
michael watson (IAH-C)
- [BioC] Re: [S] Error in clustering procedure
Prof Brian Ripley
- [BioC] Re: [S] Error in clustering procedure
michael watson (IAH-C)
- [BioC] Re: [S] Error in clustering procedure
michael watson (IAH-C)
- [BioC] Re: [S] Error in clustering procedure
Ramon Diaz-Uriarte
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] Re: [S] Error in clustering procedure
Liaw, Andy
- [BioC] Re: [S] Error in clustering procedure
Stephen Henderson
- [BioC] Re: [S] Error in clustering procedure
cstrato
- [BioC] RE: Advice on print-tip normalization
Reimers, Mark (NIH/NCI)
- [BioC] RE: Advice on print-tip normalization
Gordon K Smyth
- [BioC] RE: Advice on print-tip normalization
Ramon Diaz-Uriarte
- [BioC] Re: Advice on print-tip normalization
Gene Cutler
- [BioC] Re: Advice on print-tip normalization
Adaikalavan Ramasamy
- [BioC] RE: Advice on print-tip normalization
Gene Cutler
- [BioC] Re: Bioconductor Digest, Vol 19, Issue 26
Eric
- [BioC] RE: Errors with -Inf
michael watson (IAH-C)
- [BioC] RE: Errors with -Inf
Gordon K Smyth
- [BioC] Re: LimmaGUI Background corrections
Gordon K Smyth
- [BioC] Re: LimmaGUI Background corrections
James Wettenhall
- [BioC] Re: LimmaGui on Mac OSX (version 10.3.5)
James Wettenhall
- [BioC] RE: Normalising divergent samples.
Matthew Hannah
- [BioC] RE: RMA normalization
Reimers, Mark (NIH/NCI)
- [BioC] RE: RMA normalization
Dalphin, Mark
- [BioC] RE: RMA normalization
Matthew Hannah
- [BioC] RE: RMA normalization
w.huber at dkfz-heidelberg.de
- [BioC] Re: Unequally spaced replicates in limma - "sort your MA
object by gene ID "
Saroj Mohapatra
- [BioC] Read.maimages question
michael watson (IAH-C)
- [BioC] Read.maimages question
Gordon K Smyth
- [BioC] Read.maimages question
Gordon Smyth
- [BioC] Read.maimages question
michael watson (IAH-C)
- [BioC] Reading mev files into bioC
Tarca Adi Laurentiu
- [BioC] Recent changes to Bioconductor packages
madman at jimmy.harvard.edu
- [BioC] Recent changes to Bioconductor packages
madman at jimmy.harvard.edu
- [BioC] Regarding Rgraphviz compilation error
Saurin Jani
- [BioC] Regarding Rgraphviz compilation error
Jeff Gentry
- [BioC] Regarding Rgraphviz compilation error
Saurin Jani
- [BioC] Regarding Rgraphviz compilation error
Jeff Gentry
- [BioC] Rgraphviz + graphviz 1.12.1 compilation error
Saurin Jani
- [BioC] Rgraphviz + graphviz 1.12.1 compilation error
Jeff Gentry
- [BioC] Rgraphviz Error : Rgraphviz.c: In function
`Rgraphviz_agopen':
Saurin Jani
- [BioC] Rgraphviz install issues
Andrew Beckerman
- [BioC] Rgraphviz install issues
Jeff Gentry
- [BioC] Rgraphviz: read .dot file
Xiao-Jun Ma
- [BioC] Rgraphviz: read .dot file
Vincent Carey 525-2265
- [BioC] RMA normalization
Adaikalavan Ramasamy
- [BioC] RMA normalization
Adaikalavan Ramasamy
- [BioC] RMA normalization
Fangxin Hong
- [BioC] RMA normalization
Hairong Wei
- [BioC] RMA outline
Lawrence-Paul Petalidis
- [BioC] rma question
Hairong Wei
- [BioC] rma question
Hairong Wei
- [BioC] rma question
Adaikalavan Ramasamy
- [BioC] SAM: the fudge factor in Siggenes and Excel
Caimiao Wei
- [BioC] SE and memory problems
Florence Combes
- [BioC] SE in RMA and GCRMA
Florence Combes
- [BioC] SE in RMA and GCRMA
Davide
- [BioC] SE in RMA and GCRMA
Zhijin Wu
- [BioC] Selecting p-value cutoffs for differential expression
Matthew Hannah
- [BioC] Selecting p-value cutoffs for differential expression
Ramon Diaz-Uriarte
- [BioC] Selecting p-value cutoffs for differential expression
Suresh Gopalan
- [BioC] Selecting p-value cutoffs for differential expression
Suresh Gopalan
- [BioC] superpc - 'group' and 'Cox score'
Liu, Xin
- [BioC] superpc - 'group' and 'Cox score'
Liu, Xin
- [BioC] superpc - 'group' and 'Cox score'
James W. MacDonald
- [BioC] SV:Package for ArrayWoRx output-files
Per Gregersen
- [BioC] Swiss-Prot to gene annotation translation/conversion
Kimpel, Mark W
- [BioC] Swiss-Prot to gene annotation translation/conversion
Sean Davis
- [BioC] Terminology was RE: RMA normalization
Ben Bolstad
- [BioC] Terminology was RE: RMA normalization
w.huber at dkfz-heidelberg.de
- [BioC] Terminology was RE: RMA normalization
Laurent Gautier
- [BioC] to extract just some columns of an exprsSet
Florence Combes
- [BioC] to extract just some columns of an exprsSet
Vincent Carey 525-2265
- [BioC] Trouble Loading RBGL
Jeff Lande
- [BioC] Trouble Loading RBGL
Jeff Gentry
- [BioC] Unequally spaced replicates in limma
michael watson (IAH-C)
- [BioC] Unequally spaced replicates in limma
Gordon K Smyth
- [BioC] Unequally spaced replicates in limma
michael watson (IAH-C)
- [BioC] Unequally spaced replicates in limma
Gordon Smyth
- [BioC] Unequally spaced replicates in limma
Elizabeth Brooke-Powell
- [BioC] Unequally spaced replicates in limma - "sort your MA
object by gene ID "
Jakob Hedegaard
- [BioC] Unequally spaced replicates in limma - 'sort your MA
object by gene ID '
Gordon K Smyth
- [BioC] Unique probes on all human affy chips
S Peri
- [BioC] Unique probes on all human affy chips
S Peri
- [BioC] Unique probes on all human affy chips
Adaikalavan Ramasamy
- [BioC] Unique probes on all human affy chips
Robert Gentleman
- [BioC] Unique probes on all human affy chips
Laurent Gautier
- [BioC] Unique probes on all human affy chips
Laurent Gautier
- [BioC] using getPMID with non-affy data
Kimpel, Mark W
- [BioC] using getPMID with non-affy data
Robert Gentleman
- [BioC] using getPMID with non-affy data
Sean Davis
- [BioC] using mat.samp in siggenes
Kathleen Kerr
- [BioC] using mat.samp in siggenes
James W. MacDonald
- [BioC] using mat.samp in siggenes
Holger Schwender
- [BioC] using mat.samp in siggenes
Kathleen Kerr
- [BioC] using mat.samp in siggenes
Holger Schwender
- [BioC] Weight functions for Agilent chips (limma)
Malard, Joel M
- [BioC] Weight functions for Agilent chips (limma)
Giovanni Coppola
- [BioC] Weight functions for Agilent chips (limma)
Malard, Joel M
- [BioC] Weight functions for Agilent chips (limma)
Giovanni Coppola
- [BioC] which library - identify gene expression markers using
Bayesian
Liu, Xin
- [Fwd: RE: [BioC] RMA normalization]
Adaikalavan Ramasamy
- Flagging spots (was: [BioC] Bioconductor documentation
Gordon Smyth
- Fw: [BioC] Affy Bioconductor with Rat230_2 chips
Ali A. Pirani
- Fwd: Re: [BioC] Problem with gls.series in limma
Gordon Smyth
- GOT IT Re: [BioC] to extract just some columns of an exprsSet
Florence Combes
Last message date:
Thu Sep 30 19:54:11 CEST 2004
Archived on: Thu Sep 30 19:53:24 CEST 2004
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