November 2005 Archives by thread
Starting: Tue Nov 1 02:33:09 CEST 2005
Ending: Wed Nov 30 23:52:27 CEST 2005
Messages: 392
- [BioC] AnnBuilder problem?
Denise Mauldin
- [BioC] How to install biomaRt package on Windows XP
Wuming Gong
- [BioC] How to install biomaRt package on Windows XP
sdurinck
- [BioC] problems with biomaRt on Mac OS X (10.4.2 = Tiger)
sdurinck
- [BioC] gcrma
Bettina Harr
- [BioC] How to retrieve the genomic positions and /or orders of probes in the probe set
szhan at uoguelph.ca
- [BioC] E. coli problems: bimodality and gcrma
Jenny Drnevich
- [BioC] Help on Loading AgilentData into LIMMA
Nataliya Yeremenko
- [BioC] qvalue package: Strange distribution of q values
Dr. Reinhard Hoffmann
- [BioC] attributes of SAM files
Assa Yeroslaviz
- [BioC] cl Vector
Assa Yeroslaviz
- [BioC] Gene names
Narendra Kaushik
- [BioC] Gene names
John Zhang
- [BioC] Looking for R script to categorize genes using GO terms
fhong at salk.edu
- [BioC] R script
fhong at salk.edu
- [BioC] Help on Loading AgilentData into LIMMA
Gordon Smyth
- [BioC] Using limma with Applied Precision SoftWorx data
David Henderson
- [BioC] Help on Loading AgilentData into LIMMA
Gordon Smyth
- [BioC] normexp background correction
Edoardo Giacopuzzi
- [BioC] (no subject)
Kort, Eric
- [BioC] gcrma and custom chips
Daniel Pick
- [BioC] Bioconductor on CD-ROM
Francois Pepin
- [BioC] converting data into logical matrix
Assa Yeroslaviz
- [BioC] cross validation / bootstrap after classification
Heike Pospisil
- [BioC] cross validation / bootstrap after classification
Heike Pospisil
- [BioC] proportianal hazard models
Heike Pospisil
- [BioC] class comparison with SAM
Stefania Pilati
- [BioC] Job openings in computing and statistics
Hulin Wu
- [BioC] single-array error model for chip-on-chip experiment
Duhaime Johanne
- [BioC] Trouble querying pubmed on strings
Ken Termiso
- [BioC] Rdbi
Hrishikesh Deshmukh
- [BioC] How to write "matchprobes" result(list of vector) to a table?
Lingsheng Dong
- [BioC] Gene names
Christopher Wilkinson
- [BioC] Estrogen data error in genelist
Thomas Curtis
- [BioC] normexp background correction
Gordon K Smyth
- [BioC] grDevices under Linux
Assa Yeroslaviz
- [BioC] expresso dies on list.files
Kort, Eric
- [BioC] normalization hgu133a and hgu133b: gcrma
Sabrina Carpentier
- [BioC] Draw volcanoplot in Limma
Edoardo Giacopuzzi
- [BioC] Order of probesets in an exprSet
Jamain, Adrien J
- [BioC] paired t test for siblings?
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] problem with annaffy aafFunction function
Kimpel, Mark William
- [BioC] problem with annaffy aafFunction function
John Zhang
- [BioC] Help on Loading AgilentData into LIMMA
Nataliya Yeremenko
- [BioC] writing of /usr/lib/R
Michael Green
- [BioC] Help on Loading AgilentData into LIMMA
Gordon K Smyth
- [BioC] [Bioc-devel] Draw volcanoplot in Limma
Gordon K Smyth
- [BioC] Help on hclust function
madhurima bhattacharjee
- [BioC] problem with hclust
madhurima bhattacharjee
- [BioC] writing of /usr/lib/R
Liaw, Andy
- [BioC] Determining Synergy in MA expts
Lance Palmer
- [BioC] getting absolute expression values for cDNA arrays
Irina Borodina
- [BioC] Creating a CDFenv without cdf file
Nicholas Lewin-Koh
- [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array
Earl F. Glynn
- [BioC] Training Program at Texas A&M
Marina Vannucci
- [BioC] Roomity.com v 1.5 is a web 2.01
shenanigans
- [BioC] averaging replicates within arrays
alex lam (RI)
- [BioC] Help on Loading AgilentData into LIMMA
Gordon Smyth
- [BioC] Help on Loading AgilentData into LIMMA
Nataliya Yeremenko
- [BioC] averaging replicates within arrays
Gordon Smyth
- [BioC] normexp background correction
Gordon Smyth
- [BioC] problem with cuttree
madhurima bhattacharjee
- [BioC] Limma two group layout; two approaches but different results
Björn Usadel
- [BioC] writing of /usr/lib/R
Liaw, Andy
- [BioC] averaging replicates within arrays
alex lam (RI)
- [BioC] FRD : package fdrame vs multtest
Nicolas Servant
- [BioC] grep GOID, R problem or my problem?
fhong at salk.edu
- [BioC] beta7
kirk hammet
- [BioC] AffyBatch <-> exprSet
Igor Androv
- [BioC] Limma two group layout; two approaches but different results
Gordon K Smyth
- [BioC] writing of /usr/lib/R
Shi, Tao
- [BioC] AffyBatch <-> exprSet
Kort, Eric
- [BioC] Quality Images Website moved
Ben Bolstad
- [BioC] Low Ratio values in LIMMA
Nataliya Yeremenko
- [BioC] Problem compiling hexbin with gcc 4.0.2
David Henderson
- [BioC] proportianal hazard models
Kort, Eric
- [BioC] Problem compiling hexbin with gcc 4.0.2
David Henderson
- [BioC] Problem compiling hexbin with gcc 4.0.2
David Henderson
- [BioC] mapping kegg gene ids to probeset
Dr.Mayhaus Manuel
- [BioC] S/N ratio in microarrays
narinder.singh at diagenic.com
- [BioC] repeated measures in limma?
rob foxall (IFR)
- [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array
Crispin Miller
- [BioC] loading Bioconductor - error message
Natalie Twine
- [BioC] Help regarding mas5 normalization
Nayeem Quayum
- [BioC] Question about heatmap
Giovanni d'Ario
- [BioC] normexp backgroundCorrect problem
Lance Palmer
- [BioC] [Limma] M value in contrast test
Marcelo Luiz de Laia
- [BioC] Which method best fit nylon single channel technology ?
TEXTORIS Julien
- [BioC] ReadAffy() for customized Affy chips
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] MAplot in affyPLM library
Simon Lin
- [BioC] Design question in LIMMA
Nataliya Yeremenko
- [BioC] Change to limma::eBayes
Gordon Smyth
- [BioC] Which method best fit nylon single channel technology ?
TEXTORIS Julien
- [BioC] Gene Mapping on Chrosmosomes
Hrishikesh Deshmukh
- [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array
Jenny Drnevich
- [BioC] GCRMA with custom chips
Daniel Pick
- [BioC] [Limma] M value in contrast test
James W. MacDonald
- [BioC] ReadAffy() for customized Affy chips
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] Resourcerer warnings
Francois Pepin
- [BioC] Design question in LIMMA
Gordon K Smyth
- [BioC] affy troubles
YY Teo
- [BioC] Compendia
Wolfgang Huber
- [BioC] lmFit and block argument for technical replicates
Carolyn Fitzsimmons
- [BioC] | Correlation | > 1 (limma)
Naomi Altman
- [BioC] | Correlation | > 1 (limma)
Gordon Smyth
- [BioC] | Correlation | > 1 (limma)
Gordon Smyth
- [BioC] normexp backgroundCorrect problem
Gordon Smyth
- [BioC] p-value from geneSetTest in Limma
Na, Ren
- [BioC] how to configure "pkgconfig"
shen bairong
- [BioC] how to configure "pkgconfig"
shen bairong
- [BioC] BioC 1.6 Release unavailable
Xuejun Liu
- [BioC] Small bug in function 'countskip.FASTA.entries' from package 'altcdfenvs'
Norman Pavelka
- [BioC] affymetrix pig annotation data
Morten Mattingsdal
- [BioC] gpr one color
kirk hammet
- [BioC] gpr one color
Paquet, Agnes
- [BioC] affymetrix pig annotation data
John Zhang
- [BioC] AffyPLM: MAplot
Simon Lin
- [BioC] BioC 1.6 Release unavailable
Kort, Eric
- [BioC] expresso still dying on list.files()
Kort, Eric
- [BioC] expresso still dying on list.files()--solved
Kort, Eric
- [BioC] How to deal with technical replicates in limmaGUI?
Cecilia McGregor
- [BioC] (no subject)
Cecilia McGregor
- [BioC] Bug in maNormNN
Tarca, Adi
- [BioC] HGU133atag_probe
Lana Schaffer
- [BioC] question about the code in Lab 4 - Differential Expression and Linear Modeling using limma(Estrogen Data) on http://www.bioconductor.org/workshops/2005/BioC2005/labs/lab01/estrogen.html
Na, Ren
- [BioC] hgu133atag-older version worked
Lana Schaffer
- [BioC] question about the code in Lab 4 - Differential Expression and Linear Modeling using limma(Estrogen Data)
Gordon Smyth
- [BioC] hgu133atag-older version worked
James MacDonald
- [BioC] GEO + SOFT files
Stephen Henderson
- [BioC] BiomaRt connection error
Wu, Xiwei
- [BioC] Single Channel Analysis
Naomi Altman
- [BioC] GCRMA with custom chips
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] limma's eBayes error: No residual degrees of freedom in linear model
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] (no subject)
Khan, Sohail
- [BioC] repeated measures in limma?
michael watson (IAH-C)
- [BioC] how to match the identifiers in multiple microarray data sets
weinong han
- [BioC] Creating an object of class exprSet
Khan, Sohail
- [BioC] Small bug in function 'countskip.FASTA.entries' from package altcdfenvs
Norman Pavelka
- [BioC] Bioinformatics Jobs at ArraDx
Proutski, Vitali
- [BioC] BiomaRt connection error
Wu, Xiwei
- [BioC] limma, spot and technical replicates
Cecilia McGregor
- [BioC] limma's eBayes error: No residual degrees of freedom in linear model
Gordon Smyth
- [BioC] how to combine the different expression values in Meta Analysis of microrrays
weinong han
- [BioC] Small bug in function 'countskip.FASTA.entries' from package altcdfenvs
Norman Pavelka
- [BioC] limma, spot and technical replicates
STKH (Steen Krogsgaard)
- [BioC] lmFit simple design or contrast
Beatriz
- [BioC] Limma lmFit simple design or contrast
Beatriz
- [BioC] Limma lmFit simple design or contrast
Beatriz
- [BioC] MACAT gene list. Over and under expressed
Giulio Di Giovanni
- [BioC] Fwd: Statistical Computing Position
A.J. Rossini
- [BioC] limma's eBayes error: No residual degrees of freedom in linear model
Li,Qinghong,ST.LOUIS,Molecular Biology
- [BioC] Rosetta vs Limma
Nataliya Yeremenko
- [BioC] About weight function for Agilent data
Nataliya Yeremenko
- [BioC] BiomaRt connection error
Wu, Xiwei
- [BioC] duplicateCorrelation
Devin Scannell
- [BioC] how to combine the different expression values in Meta Analysis of microrrays
weinong han
- [BioC] duplicateCorrelation
Gordon Smyth
- [BioC] Rosetta vs Limma
Gordon K Smyth
- [BioC] About weight function for Agilent data
Gordon K Smyth
- [BioC] normalization the expression values
Assa Yeroslaviz
- [BioC] lmFit simple design or contrast
Beatriz
- [BioC] getGene in biomaRt package
James MacDonald
- [BioC] LIMMA makeContrast one test and two controls
Robert Ivanek
- [BioC] limma's eBayes error: No residual degrees of freedom in linear model
Gordon K Smyth
- [BioC] [Limma] Correcting Dye swap effect
Ron Ophir
- [BioC] [Limma] Correcting Dye swap effect
Gordon K Smyth
- [BioC] getGene in biomaRt package
sdurinck
- [BioC] limma's eBayes error: No residual degrees of freedom in linear model
Gordon Smyth
- [BioC] limma Normalization question
Cecilia McGregor
- [BioC] BioC v1.7 and R version?
Stan Smiley
- [BioC] limma Normalization question
Gordon K Smyth
- [BioC] limma Normalization question
Cecilia McGregor
- [BioC] limma Normalization question
Gordon Smyth
- [BioC] Looking for HuEx-1_0-st-v2.cdf File
Natalia Becker
- [BioC] GOstats/tkWidgets/gcrma conflict
mattia
- [BioC] How to match Locus IDs with Gene Ontology IDs?
Earl F. Glynn
- [BioC] Looking for HuEx-1_0-st-v2.cdf File
Natalia Becker
- [BioC] How to save jpegs of all MAplots of an affybatch
Giulio Di Giovanni
- [BioC] AnnBuilder: use local gene2accession file
Andrej Kastrin
- [BioC] AnnBuilder: use local gene2accession file
John Zhang
- [BioC] omit row dendrogram in heatmap
Georg Otto
- [BioC] How to make a CDF package from an alternative CDF environment
Norman Pavelka
- [BioC] How to tell the "matchprobes" function to match PM probe only?
Lingsheng Dong
- [BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug
Gordon Smyth
- [BioC] how to export the selected data?
weinong han
- [BioC] Cel -> MAGE-ML
Steffen Durinck
- [BioC] AnnBuilder question: about how to retrieve information when using a built package?
Johan Lindberg
- [BioC] Problem with sp.between
Jamain, Adrien J
- [BioC] omit row dendrogram in heatmap
Lourdes Peña Castillo
- [BioC] [AnnBuilder] How to use/load generated annotation packages
Rainer Grohmann
- [BioC] Again on heatmap clusters - dChip style, Pearson's distance. Which solutions ?
Giulio Di Giovanni
- [BioC] What to do with multiple probes?
krasikov at science.uva.nl
- [BioC] Biobase/affy installation problem in linux
Anja Schiel
- [BioC] Problems checking code for "computeExprSet"
Benjamin Otto
- [BioC] Problems checking code for "computeExprSet"
Stephen Henderson
- [BioC] normalization of colonCA data
pmt1rew at leeds.ac.uk
- [BioC] Fwd: limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug
Gordon Smyth
- [BioC] How to write a text file of a pamr.confusion table ?
Giulio Di Giovanni
- [BioC] why S-Score is not poppular like T-test pvalue and BH FDR , which is OK to use?
Saurin Jani
- [BioC] calculating replicate average in exprs(eset)
Georg Otto
- [BioC] average linkage clustering in Eisen's Cluster vs. that in hclust
Wittner, Ben
- [BioC] MedlineR - Error in xmlRoot
Andrej Kastrin
- [BioC] Problem with sp.between
Jamain, Adrien J
- [BioC] normexp (limma) failure?
bregje wertheim
- [BioC] Channel splitting problem
krasikov at science.uva.nl
- [BioC] normexp (limma) failure?
bregje wertheim
- [BioC] normexp (limma) failure?
bregje wertheim
- [BioC] Limma toptable question
Hua Weng
- [BioC] Affy autodownload cdf problem
Sean Davis
- [BioC] merging fit and MA objects
Guoneng Zhong
Last message date:
Wed Nov 30 23:52:27 CEST 2005
Archived on: Thu Dec 1 18:32:51 CEST 2005
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