July 2006 Archives by author

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Starting: Sat Jul 1 09:50:34 CEST 2006
Ending: Mon Jul 31 20:55:11 CEST 2006
Messages: 309

• [BioC] biomaRt error: useMart fails   michael watson (IAH-C)
• [BioC] biomaRt error: useMart fails   michael watson (IAH-C)
• [BioC] Unable to use biomaRt because Rcurl doesn't pick up my proxy server address   michael watson (IAH-C)
• [BioC] last call for Boston bioc Training, 13-15 july, content revised   Vincent Carey 525-2265
• [BioC] 2 color data...   Naomi Altman
• [BioC] 2 color data...   Naomi Altman
• [BioC] another question   Naomi Altman
• [BioC] Limma Modeling   Naomi Altman
• [BioC] methods for Differential expression   Naomi Altman
• [BioC] Your FANTASTIC help with soybean   Alvord, Greg (DMS) [Contr]
• [BioC] Quick illumina question   Lynn Amon
• [BioC] spatial plot image of foreground minus background   Andre
• [BioC] Interface to BASE microarray data   Henrik Bengtsson
• [BioC] Affymetrix exon arrays?   Henrik Bengtsson
• [BioC] Missing chromosomal locations in hgu133a package   Hilmar Berger
• [BioC] Missing chromosomal locations in hgu133a package   Hilmar Berger
• [BioC] Analysing categorical CGH data   Richard Birnie
• [BioC] tiling/SNP microarrays   Jeffrey Blanchard
• [BioC] Drosophila Genome 2.0 annaffy annotation   Marco Blanchette
• [BioC] Dist of exprSet object   Marco Blanchette
• [BioC] Dist of exprSet object   Marco Blanchette
• [BioC] Dist of exprSet object   Marco Blanchette
• [BioC] normalize.AffyBatch.quantiles and NA values   Ben Bolstad
• [BioC] Dist of exprSet object   Ben Bolstad
• [BioC] Reference for Volcano plot   Anthony Bosco
• [BioC] Gene set analysis/Global test with 3 replicates   Anthony Bosco
• [BioC] marrayNorm to exprSet object   Daniel Brewer
• [BioC] marray and gathering additional information from GenePix GPR file   Daniel Brewer
• [BioC] marrayNorm to exprSet object   Daniel Brewer
• [BioC] marray and gathering additional information from GenePix GPR file   Daniel Brewer
• [BioC] marray and gathering additional information from GenePix GPR file   Daniel Brewer
• [BioC] Interface to BASE microarray data   Daniel Brewer
• [BioC] Limma Modeling   Katarzyna Bryc
• [BioC] analysis of timeseries with treatment effect   Carlos Calderon
• [BioC] problem with ReadAffy   Sabrina Carpentier
• [BioC] RES: promotor tilingArray   Carvalho, Benilton
• [BioC] problem to load the "matchprobes" pkg   Florence Combes
• [BioC] problem to load the "matchprobes" pkg   Florence Combes
• [BioC] problem in gcrma with phenoData   Florence Combes
• [BioC] problem with ReadAffy   Florence Combes
• [BioC] OT: question about plots, general R, really...   Ana Conesa
• [BioC] AnnBuilder package: problem with gbNRef   Craddock, Richard C. (CDC/NCID/VR) (CTR)
• [BioC] AnnBuilder package: problem with gbNRef   Craddock, Richard C. (CDC/NCID/VR) (CTR)
• [BioC] AnnBuilder package: problem with gbNRef   Craddock, Richard C. (CDC/NCID/VR) (CTR)
• [BioC] AnnBuilder package: problem with gbNRef - don't put quotes in basefile!   Craddock, Richard C. (CDC/NCID/VR) (CTR)
• [BioC] retrieve the gene symbols, full names etc given list of Entrez Gene IDs   Sean Davis
• [BioC] affyio   Sean Davis
• [BioC] affyio   Sean Davis
• [BioC] marrayNorm to exprSet object   Sean Davis
• [BioC] Annotation   Sean Davis
• [BioC] problem to obtain exprset using GEOquery   Sean Davis
• [BioC] tiling/SNP microarrays   Sean Davis
• [BioC] How to create expression data packages   Sean Davis
• [BioC] 2 color data...   Sean Davis
• [BioC] Limma Modeling   Sean Davis
• [BioC] GEOquery   Sean Davis
• [BioC] Quick illumina question   Sean Davis
• [BioC] Quick illumina question   Sean Davis
• [BioC] Problem conduction MAS5 on HGU133B data   Sean Davis
• [BioC] how to handle pooled replicate?   Sean Davis
• [BioC] marray and gathering additional information fromGenePixGPR file   Marcus Davy
• [BioC] marray and gathering additional information fromGenePixGPR file   Marcus Davy
• [BioC] Dist of exprSet object   Marcus Davy
• [BioC] new codelink annotation packages.   Diego Diez
• [BioC] moderated t statistic in limma   Jenny Drnevich
• [BioC] marray and gathering additional information from GenePix GPR file   Jenny Drnevich
• [BioC] marray and gathering additional information from GenePix GPR file   Jenny Drnevich
• [BioC] marray and gathering additional information fromGenePixGPR file   Jenny Drnevich
• [BioC] 2 color data...   Jenny Drnevich
• [BioC] Limma function plotDensities question   Jenny Drnevich
• [BioC] R/beadarray and array decoding files   Mark Dunning
• [BioC] Problem with getBM function in biomaRt package   Steffen Durinck
• [BioC] biomaRt error: useMart fails   Steffen Durinck
• [BioC] biomaRt error in getGene   Steffen Durinck
• [BioC] biomaRt error in getGene   Steffen Durinck
• [BioC] methods for Differential expression   E Motakis, Mathematics
• [BioC] Problem of using Affy!   Seth Falcon
• [BioC] Rgraphviz: Setting the edge width   Seth Falcon
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Seth Falcon
• [BioC] bioconductor install problem   Seth Falcon
• [BioC] Annotation   Seth Falcon
• [BioC] no direct or inherited method for function phenoData   Seth Falcon
• [BioC] no direct or inherited method for function phenoData   Seth Falcon
• [BioC] Errors using biocLite on Apple OS X   Seth Falcon
• [BioC] Too many open files error with groupName = "all" in biocLite() call on Apple OS X   Seth Falcon
• [BioC] poplarcdf uninstallable   Seth Falcon
• [BioC] MySQL databases offering gene expression, esp. toxicogenomics data   Seth Falcon
• [BioC] automatically checking the version of a BioC package   Seth Falcon
• [BioC] chips/array supported by BioC   Seth Falcon
• [BioC] Problem conduction MAS5 on HGU133B data   Seth Falcon
• [BioC] Drosophila Genome 2.0 annaffy annotation   Seth Falcon
• [BioC] Affymetrix exon arrays?   Seth Falcon
• [BioC] problem with GO annotation data   Seth Falcon
• [BioC] problem with GO annotation data   Seth Falcon
• [BioC] Separate channels and common references   Francesco Favero
• [BioC] Problem of using Affy!   Zeny Feng
• [BioC] Display Chromosome-bands in a plot   Furge, Kyle
• [BioC] Repository for Bioconductor annotation packages   Daniel Gatti
• [BioC] Repository for Bioconductor annotation packages   Daniel Gatti
• [BioC] Repository for Bioconductor annotation packages   Daniel Gatti
• [BioC] How to create expression data packages   Robert Gentleman
• [BioC] affypdnn problem   Kathakali Ghosh
• [BioC] HELP WITH DATA   Alberto Goldoni
• [BioC] problem to obtain exprset using GEOquery   Alberto Goldoni
• [BioC] question for the prediction of the tRNA secondary structure   Alberto Goldoni
• [BioC] MySQL databases offering gene expression, esp. toxicogenomics data   N. Goodacre
• [BioC] automatically checking the version of a BioC package   Gregor Gorjanc
• [BioC] Problem of using Affy!   Kasper Daniel Hansen
• [BioC] bioconductor install problem   Kasper Daniel Hansen
• [BioC] Make a cdf package for unconventional Affymetrix chips   Kasper Daniel Hansen
• [BioC] problem to obtain exprset using GEOquery   Stephen Henderson
• [BioC] questions about RLMM   Yen Tsung Huang
• [BioC] vsn and microarray blank spots   Wolfgang Huber
• [BioC] Test: Treatment leads to more variance in groups?   Wolfgang Huber
• [BioC] How to retrieve locusID from ensembl using biomaRt package version 1.6.0   Wolfgang Huber
• [BioC] Dist of exprSet object   Wolfgang Huber
• [BioC] BH vs BY in p.adjust   Wolfgang Huber
• [BioC] BH vs BY in p.adjust   Wolfgang Huber
• [BioC] no direct or inherited method for function phenoData   Lina Hultin-Rosenberg
• [BioC] no direct or inherited method for function phenoData   Lina Hultin-Rosenberg
• [BioC] no direct or inherited method for function phenoData   Lina Hultin-Rosenberg
• [BioC] chickencdf in qcEnv   Lina Hultin-Rosenberg
• [BioC] Rgraphviz: Setting the edge width   Søren Højsgaard
• [BioC] breast tissue cel files   Rafael A. Irizarry
• [BioC] questions about RLMM   Rafael A. Irizarry
• [BioC] a question on creating model.matrix using limma   Srinivas Iyyer
• [BioC] How to create expression data packages   Srinivas Iyyer
• [BioC] how to handle pooled replicate?   Jianping Jin
• [BioC] affyio   Khan, Sohail
• [BioC] affyio   Khan, Sohail
• [BioC] Point size for the function plotPrintTipLoess()   Khan, Sohail
• [BioC] ABPackageBuilder not building GO package?   Eric J. Kort
• [BioC] ABPackageBuilder not building GO package?   Eric J. Kort
• [BioC] Unable to use biomaRt because Rcurl doesn't pick up my proxy server address   Duncan Temple Lang
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Nianhua Li
• [BioC] [biocannotation] Question about mgu74a   Nianhua Li
• [BioC] ABPackageBuilder not building GO package?   Nianhua Li
• [BioC] Missing chromosomal locations in hgu133a package   Nianhua Li
• [BioC] ABPackageBuilder not building GO package?   Nianhua Li
• [BioC] AnnBuilder package: problem with basefile type of   Nianhua Li
• [BioC] AnnBuilder package: problem with gbNRef   Nianhua Li
• [BioC] AnnBuilder package: problem with gbNRef   Nianhua Li
• [BioC] problem with GO annotation data   Nianhua Li
• [BioC] problem with GO annotation data   Nianhua Li
• [BioC] problem with GO annotation data   Nianhua Li
• [BioC] GEOquery   LUIS F MENEZES
• [BioC] retrieve the gene symbols, full names etc given list of Entrez Gene IDs   James W. MacDonald
• [BioC] about understanding contrast matrix   James W. MacDonald
• [BioC] Run GOHyperG on yeast without specifying a chip   James W. MacDonald
• [BioC] Problem with getBM function in biomaRt package   James W. MacDonald
• [BioC] OT: question about plots, general R, really...   James W. MacDonald
• [BioC] problem to load the "matchprobes" pkg   James W. MacDonald
• [BioC] problem in gcrma with phenoData   James W. MacDonald
• [BioC] affyio   James W. MacDonald
• [BioC] a question on creating model.matrix using limma   James W. MacDonald
• [BioC] annotation package: get probenames from gene names   James W. MacDonald
• [BioC] Repository for Bioconductor annotation packages   James W. MacDonald
• [BioC] Repository for Bioconductor annotation packages   James W. MacDonald
• [BioC] Repository for Bioconductor annotation packages   James W. MacDonald
• [BioC] no direct or inherited method for function phenoData   James W. MacDonald
• [BioC] no direct or inherited method for function phenoData   James W. MacDonald
• [BioC] 2 color data...   James W. MacDonald
• [BioC] qc function missing in Linux version of simpleaffy   James W. MacDonald
• [BioC] questions about RLMM   James W. MacDonald
• [BioC] Error: cannot allocate vector of size ...   James W. MacDonald
• [BioC] Problem regardign ReadAffy()   James W. MacDonald
• [BioC] Drosophila Genome 2.0 annaffy annotation   James W. MacDonald
• [BioC] Dist of exprSet object   James W. MacDonald
• [BioC] OT: question about plots, general R, really...   Martin Maechler
• [BioC] Errors using biocLite on Apple OS X   Steven McKinney
• [BioC] Errors using biocLite on Apple OS X   Steven McKinney
• [BioC] Too many open files error with groupName = "all" in biocLite() call on Apple OS X   Steven McKinney
• [BioC] Errors using biocLite on Apple OS X   Steven McKinney
• [BioC] lmFit object limma   Andrew Mcdonagh
• [BioC] limma advice required. Investigating the amplification of small sample RNA   Andrew Mcdonagh
• [BioC] limma advice required. Investigating the amplification of small sample RNA   Andrew Mcdonagh
• [BioC] bioconductor install problem   Amy Mikhail
• [BioC] marrayNorm to exprSet object   Martin Morgan
• [BioC] [SPAM?] Bioconductor Digest, Vol 41, Issue 22 (Out of Office)   Todd Nick
• [BioC] Gene set analysis/Global test with 3 replicates   Oosting, J. (PATH)
• [BioC] Display Chromosome-bands in a plot   Oosting, J. (PATH)
• [BioC] Quick illumina question   Oosting, J. (PATH)
• [BioC] promotor tilingArray   Ron Ophir
• [BioC] [limma] 3-Way Factorial design   Ron Ophir
• [BioC] Test: Treatment leads to more variance in groups?   Benjamin Otto
• [BioC] Display Chromosome-bands in a plot   Benjamin Otto
• [BioC] annotation package: get probenames from gene names   Georg Otto
• [BioC] biomaRt error in getGene   Georg Otto
• [BioC] biomaRt error in getGene   Georg Otto
• [BioC] biomaRt error in getGene   Georg Otto
• [BioC] installing Rgraphviz on FC5   Herve Pages
• [BioC] Repository for Bioconductor annotation packages   Herve Pages
• [BioC] Errors using biocLite on Apple OS X   Herve Pages
• [BioC] Dist of exprSet object   Francois Pepin
• [BioC] Limma function plotDensities question   Pete
• [BioC] Affymetrix expert   Ulrich Pfeffer
• [BioC] error in annotate-function of cellHTS package   Klaus-Peter Pleissner
• [BioC] error in annotate-function of cellHTS package (2. trial)   Klaus-Peter Pleissner
• [BioC] Problem regardign ReadAffy()   Nayeem Quayum
• [BioC] Problem conduction MAS5 on HGU133B data   Nayeem Quayum
• [BioC] qc function missing in Linux version of simpleaffy   Wolfgang Raffelsberger
• [BioC] biomaRt error in getGene   Johannes Rainer
• [BioC] installing Rgraphviz on FC5   Johannes Rainer
• [BioC] moderated t statistic in limma   Pedro López Romero
• [BioC] moderated t statistic in limma   Pedro López Romero
• [BioC] Affymetrix exon arrays?   Jesse Salisbury
• [BioC] Repository for Bioconductor annotation packages   Keith Satterley
• [BioC] installing Rgraphviz on FC5   Stefan Schmidt
• [BioC] artifact in MA plots   Matthew Scholz
• [BioC] Reference for Volcano plot   William Shannon
• [BioC] Quantile Volcano Plots   William Shannon
• [BioC] simpleaffy and rhesuscdf - error.   Sharon
• [BioC] Building annotation packages for plant species   Simon, Reinhard (CIP)
• [BioC] Building annotation packages for plant species   Simon, Reinhard (CIP)
• [BioC] Error: cannot allocate vector of size ...   M L Smith
• [BioC] analysis of timeseries with treatment effect   Gordon Smyth
• [BioC] Bioconductor Digest, Vol 41, Issue 4   Gordon Smyth
• [BioC] Reference for Volcano plot   Gordon Smyth
• [BioC] color venn diagrams   Gordon Smyth
• [BioC] limma advice required. Investigating the amplification of small sample RNA   Gordon Smyth
• [BioC] limma advice required. Investigating the amplification of small sample RNA   Gordon K Smyth
• [BioC] BH vs BY in p.adjust + FDR interpretation   Gordon K Smyth
• [BioC] OT: question about plots, general R, really...   Ulrik Stervbo
• [BioC] OT: question about plots, general R, really...   Ulrik Stervbo
• [BioC] Cell cycle analysis of FACS data   Ulrik Stervbo
• [BioC] OT: question about plots, general R, really...   Ido M. Tamir
• [BioC] [Rd] Errors using biocLite on Apple OS X   Simon Urbanek
• [BioC] HELP WITH DATA   Björn Usadel
• [BioC] limma: read.maimages possibility to warn the user?   Björn Usadel
• [BioC] BIRD: Fiest internation conference : Bioinformatics in Research and Development   Prof.Roland Wagner
• [BioC] poplarcdf uninstallable   Levi Waldron
• [BioC] Error: cannot allocate vector of size ...   Levi Waldron
• [BioC] error in simpleaffy qc: I'm sorry, I do not know about chip type: poplarcdf   Levi Waldron
• [BioC] Error: cannot allocate vector of size ...   Wall, Dennis Paul
• [BioC] Reference for Volcano plot   Wang, Sue Jane
• [BioC] retrieve the gene symbols, full names etc given list of Entrez Gene IDs   Luo Weijun
• [BioC] Problem with getBM function in biomaRt package   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("SYMBOL", "GENENAME", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   Luo Weijun
• [BioC] AnnBuilder package: problem with basefile type of "refseq" or "gbNRef"   Luo Weijun
• [BioC] color venn diagrams   Dane Witmer
• [BioC] color venn diagrams   Dane Witmer
• [BioC] bioconductor install problem   Di Wu
• [BioC] annotation package: get probenames from gene names   Di Wu
• [BioC] bioconductor install problem   Di Wu
• [BioC] Experimental design for mutiple groups of paired samples   Wu, Xiwei
• [BioC] Building annotation packages for plant species   John Zhang
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   John Zhang
• [BioC] Missing chromosomal locations in hgu133a package   John Zhang
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   John Zhang
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   John Zhang
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   John Zhang
• [BioC] Missing chromosomal locations in hgu133a package   John Zhang
• [BioC] Missing chromosomal locations in hgu133a package   John Zhang
• [BioC] problem with GO annotation data   John Zhang
• [BioC] Make a cdf package for unconventional Affymetrix chips   Zhang, Yang
• [BioC] Annotation   jmungal at berkeley.edu
• [BioC] 2 color data...   milesg at bu.edu
• [BioC] another question   milesg at bu.edu
• [BioC] Run GOHyperG on yeast without specifying a chip   maria at cbm.bio.uniroma2.it
• [BioC] Run GOHyperG on yeast without specifying a chip   maria at cbm.bio.uniroma2.it
• [BioC] Boxplots, different results?   ligia at ebi.ac.uk
• [BioC] OT: question about plots, general R, really...   J.delasHeras at ed.ac.uk
• [BioC] OT: question about plots, general R, really...   J.delasHeras at ed.ac.uk
• [BioC] OT: question about plots, general R, really...   J.delasHeras at ed.ac.uk
• [BioC] OT: question about plots, general R, really...   J.delasHeras at ed.ac.uk
• [BioC] OT: question about plots, general R, really...   J.delasHeras at ed.ac.uk
• [BioC] spatial plot image of foreground minus background   J.delasHeras at ed.ac.uk
• [BioC] marray and gathering additional information from GenePix GPR file   J.delasHeras at ed.ac.uk
• [BioC] marray and gathering additional information from GenePix GPR file   J.delasHeras at ed.ac.uk
• [BioC] Boxplots, different results?   J.delasHeras at ed.ac.uk
• [BioC] Boxplots, different results?   J.delasHeras at ed.ac.uk
• [BioC] Boxplots, different results?   J.delasHeras at ed.ac.uk
• [BioC] Boxplots, different results?   J.delasHeras at ed.ac.uk
• [BioC] marray and gathering additional information fromGenePixGPR file   J.delasHeras at ed.ac.uk
• [BioC] 2 color data...   J.delasHeras at ed.ac.uk
• [BioC] Problem with coloring histograms   J.delasHeras at ed.ac.uk
• [BioC] Problem with coloring histograms   J.delasHeras at ed.ac.uk
• [BioC] BH vs BY in p.adjust + FDR interpretation   lemerle at embl.de
• [BioC] BH vs BY in p.adjust   lemerle at embl.de
• [BioC] BH vs BY in p.adjust + p-value distribution   lemerle at embl.de
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   nli at fhcrc.org
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   nli at fhcrc.org
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   nli at fhcrc.org
• [BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)   nli at fhcrc.org
• [BioC] chips/array supported by BioC   stefano iacus
• [BioC] chips/array supported by BioC   stefano iacus
• [BioC] Matthew Nash has left the SGDP   M.Nash at iop.kcl.ac.uk
• [BioC] Rgraphviz: Setting the edge width   Li.Long at isb-sib.ch
• [BioC] automatically checking the version of a BioC package   burak kutlu
• [BioC] about understanding contrast matrix   yanju at liacs.nl
• [BioC] siggenes R-fold question   wxu at msi.umn.edu
• [BioC] Comparing normal versus tumor specimens from different studies   rcaloger
• [BioC] MySQL databases offering gene expression, esp. toxicogenomics data   Arne.Muller at sanofi-aventis.com
• [BioC] How to retrieve locusID from ensembl using biomaRt package version 1.6.0   swang
• [BioC] problem with GO annotation data   swang
• [BioC] problem with GO annotation data   swang
• [BioC] problem with GO annotation data   swang
• [BioC] problem with GO annotation data   swang
• [BioC] problem resolved with GO annotaion data!   swang
• [BioC] normalize.AffyBatch.quantiles and NA values   odlc at uchicago.edu
• [BioC] Bioconductor Digest, Vol 41, Issue 27   Sylvia.Merk at ukmuenster.de

Last message date: Mon Jul 31 20:55:11 CEST 2006
Archived on: Mon Jul 31 20:55:18 CEST 2006

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• More info on this list...