October 2006 Archives by thread

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Starting: Sun Oct 1 01:30:12 CEST 2006
Ending: Tue Oct 31 19:20:12 CET 2006
Messages: 286

• [BioC] Error message: no package 'file5f906952' was found   Wonjong Moon
  • [BioC] Error message: no package 'file5f906952' was found   James W. MacDonald
    • [BioC] Error message: no package 'file5f906952' was found   Goeman, J.J. (MSTAT)
• [BioC] justPlier outputs negative values   burak kutlu
• [BioC] font size problem   marco fabbri
• [BioC] Single Channel Approach for Agilent Arrays   Gaj Stan (BIGCAT)
• [BioC] justPlier outputs negative values   Alvord, Greg (DMS) [Contr]
• [BioC] Regarding error while normalizing using "loess" method   Ganiraju Manyam
  • [BioC] Regarding error while normalizing using "loess" method   James W. MacDonald
    • [BioC] Regarding error while normalizing using "loess" method   Ganiraju Manyam
      • [BioC] Regarding error while normalizing using "loess" method   James W. MacDonald
      • [BioC] Regarding error while normalizing using "loess" method   Ganiraju Manyam
      • [BioC] Regarding error while normalizing using "loess" method   Francois Pepin
• [BioC] Limma and Quantarray files   Alessio Venier
• [BioC] Question about "kidpack" installation   James W. MacDonald
• [BioC] Question about "kidpack" installation   Martin Morgan
• [BioC] probe level annotation   Shi, Tao
  • [BioC] probe level annotation   James W. MacDonald
• [BioC] probe level annotation   Shi, Tao
  • [BioC] probe level annotation   Holger Schwender
    • [BioC] probe level annotation   James W. MacDonald
• [BioC] probe level annotation   Shi, Tao
  • [BioC] probe level annotation   Holger Schwender
• [BioC] fedora core 5 x86_64 rpm extras   D.Enrique ESCOBAR ESPINOZA
• [BioC] Single Channel Approach for Agilent Arrays   Naomi Altman
  • [BioC] Single Channel Approach for Agilent Arrays   Gaj Stan (BIGCAT)
• [BioC] Affy genechips: probes many times   Saroj Mohapatra
• [BioC] combining different type affy chip data   Yanqin Yang
  • [BioC] combining different type affy chip data   Andrej Kastrin
  • [BioC] combining different type affy chip data   James W. MacDonald
• [BioC] boxplot of MM data and normalization   Shi, Tao
  • [BioC] boxplot of MM data and normalization   James W. MacDonald
• [BioC] boxplot of MM data and normalization   Shi, Tao
  • [BioC] boxplot of MM data and normalization   James W. MacDonald
• [BioC] globaltest errors   Tarun Nayar
• [BioC] Having trouble in using marray   Joo Sang Lee
  • [BioC] Having trouble in using marray   Jean Yee Hwa Yang
    • [BioC] Having trouble in using marray   Joo Sang Lee
• [BioC] Limma and Quantarray files   Gavin Kelly
• [BioC] Limma and Quantarray files   Gordon K Smyth
• [BioC] xval   mpg33 at drexel.edu
  • [BioC] xval   Wolfgang Huber
  • [BioC] xval   Robert Gentleman
• [BioC] xval   Stephen Henderson
• [BioC] Error in xval: No Direct or Inherited Method for this call   mpg33 at drexel.edu
  • [BioC] Error in xval: No Direct or Inherited Method for this call   Martin Morgan
• [BioC] limma user's guide example   Giovanni Coppola
  • [BioC] limma user's guide example   James W. MacDonald
  • [BioC] limma user's guide example   Naomi Altman
    • [BioC] limma user's guide example   Giovanni Coppola
• [BioC] BioC 1.9 is released!   Seth Falcon
• [BioC] question about SAM R package   James Anderson
  • [BioC] question about SAM R package   Jianping Jin
• [BioC] Custom arrays   Ho, Anne
  • [BioC] Custom arrays   James W. MacDonald
• [BioC] [SAGEnhaft] This library does all post analysis on SAGE or is need another software for to do?   Marcelo Luiz de Laia
  • [BioC] subsetting an eset object with a defined list   Celine Carret
    • [BioC] subsetting an eset object with a defined list   Sean Davis
      • [BioC] subsetting an eset object with a defined list   Celine Carret
      • [BioC] subsetting an eset object with a defined list   Sean Davis
      • [BioC] subsetting an eset object with a defined list   Celine Carret
      • [BioC] subsetting an eset object with a defined list   Robert Gentleman
      • [BioC] subsetting an eset object with a defined list   Jenny Drnevich
    • [BioC] subsetting an eset object with a defined list   alex lam (RI)
• [BioC] Normalization quality   alex lam (RI)
  • [BioC] Normalization quality   Sean Davis
    • [BioC] Normalization quality   alex lam (RI)
• [BioC] globaltest: pairwise design?   Goeman, J.J. (MSTAT)
• [BioC] Normalisation method worries   J.delasHeras at ed.ac.uk
• [BioC] Limma question: positive M values means upregulated in 'Treated' in this case?   Wonjong Moon
  • [BioC] Limma question: positive M values means upregulated in 'Treated' in this case?   Jenny Drnevich
• [BioC] Checking qc   alex lam (RI)
• [BioC] ChipInspector   marco fabbri
• [BioC] Affymetrix Poly-A Controls   Ann Hess
  • [BioC] Affymetrix Poly-A Controls   James W. MacDonald
• [BioC] Affymetrix exon arrays?   Steven McKinney
  • [BioC] Affymetrix exon arrays?   ltboots
• [BioC] Limma question: positive M values means upregulated in 'Treated' in this case?   Jenny Drnevich
• [BioC] How to calculate multivariate norm cdf?   James Anderson
• [BioC] gcrma and combineAffyBatch   Lo, Ken
• [BioC] gcrma and combineAffyBatch   Lo, Ken
  • [BioC] gcrma and combineAffyBatch   jean-louis.ruelle at gskbio.com
• [BioC] annotation data packages in BioC1.9   Nianhua Li
• [BioC] bioMart 1.6.3 missing mysql=TRUE in useMart   mkeehan at lic.co.nz
• [BioC] Simple affymetrix question (treated vs non-treated)   Wonjong Moon
  • [BioC] Simple affymetrix question (treated vs non-treated)   Morten Mattingsdal
• [BioC] Separate Normalizations and expression plotting   Lana Schaffer
  • [BioC] Separate Normalizations and expression plotting   Sean Davis
    • [BioC] Separate Normalizations and expression plotting   Naomi Altman
• [BioC] DSC final call and scholarships   Paul Murrell
• [BioC] Limma and Quantarray files   Alessio Venier
• [BioC] What to do with multiple probes in GSEA?   Dick Beyer
• [BioC] Custom CDFs from U mich for GeneChip Analysis   Lo, Ken
  • [BioC] Custom CDFs from U mich for GeneChip Analysis   James W. MacDonald
• [BioC] Custom CDFs from U mich for GeneChip Analysis   James W. MacDonald
• [BioC] MergeMaid version   SKALKO at clinic.ub.es
  • [BioC] MergeMaid version   alex lam (RI)
  • [BioC] MergeMaid version   Seth Falcon
• [BioC] problem updating packages OCPlus and RSNper   Kimpel, Mark William
  • [BioC] problem updating packages OCPlus and RSNper   Herve Pages
    • [BioC] problem updating packages OCPlus and RSNper   Kimpel, Mark William
• [BioC] cDNA array with 2 levels of duplication   Noah Cohen
• [BioC] Limma - error when using duplicateCorrelation   Jakob Hedegaard
• [BioC] convert .DAT to .CEL   Ana Sofia Figueiredo
  • [BioC] convert .DAT to .CEL   James W. MacDonald
• [BioC] cDNA array with 2 levels of duplication   Gordon K Smyth
• [BioC] Limma - error when using duplicateCorrelation   Gordon K Smyth
• [BioC] Limma - plotMA3by2 & imageplot3by2 - as -pdf?   Jakob Hedegaard
  • [BioC] Limma - plotMA3by2 & imageplot3by2 - as -pdf?   Jenny Drnevich
• [BioC] tcltk problem under Linux (both 32 and 64 bits)   Groot, Philip de
  • [BioC] tcltk problem under Linux (both 32 and 64 bits)   Robert Gentleman
    • [BioC] tcltk problem under Linux (both 32 and 64 bits)   Groot, Philip de
• [BioC] retrieving genomic sequences with biomaRt   J.delasHeras at ed.ac.uk
  • [BioC] retrieving genomic sequences with biomaRt   Steffen Durinck
    • [BioC] retrieving genomic sequences with biomaRt   J.delasHeras at ed.ac.uk
      • [BioC] retrieving genomic sequences with biomaRt   Steffen Durinck
• [BioC] Limma nestedF   noel0925 at sbcglobal.net
  • [BioC] Limma nestedF   James W. MacDonald
• [BioC] makePlatformDesign error   Richard Williams IV
  • [BioC] makePlatformDesign error   James W. MacDonald
• [BioC] limma: decideTests, which option to choose and nestedF pvalues   noel0925 at sbcglobal.net
• [BioC] Limma - error when using duplicateCorrelation   Gordon K Smyth
• [BioC] limma: decideTests, which option to choose and nestedF pvalues   noel0925 at sbcglobal.net
• [BioC] Limma - plotMA3by2 & imageplot3by2 - as -pdf?   Gordon Smyth
• [BioC] Limma nestedF   James W. MacDonald
  • [BioC] Limma nestedF   noel0925 at sbcglobal.net
• [BioC] create probe file from CDF?   Lo, Ken
• [BioC] FW: create probe file from CDF?   Lo, Ken
• [BioC] R/BioC workshops in Southern California   Thomas Girke
• [BioC] hs133phsentrezg metadata   De Bondt, An-7114 [PRDBE]
  • [BioC] hs133phsentrezg metadata   James W. MacDonald
• [BioC] ath1121501 and GO   Martin Olivier
  • [BioC] ath1121501 and GO   James W. MacDonald
• [BioC] matchrpobes and HGU95A mismatch   Ernest Turro
  • [BioC] matchrpobes and HGU95A mismatch   Saroj Mohapatra
    • [BioC] matchrpobes and HGU95A mismatch   Wolfgang Huber
      • [BioC] matchrpobes and HGU95A mismatch   Ernest Turro
• [BioC] CyberT versus Moderated t Comparison   Ann Hess
  • [BioC] CyberT versus Moderated t Comparison   Darlene Goldstein
• [BioC] Mismatch probe handling for exon arrays   Steven McKinney
  • [BioC] Mismatch probe handling for exon arrays   James W. MacDonald
• [BioC] array CGH   Lisa Luo
  • [BioC] R: array CGH   Alberto Goldoni
  • [BioC] array CGH   Mark Dunning
  • [BioC] array CGH   Sean Davis
    • [BioC] array CGH   Lisa Luo
      • [BioC] array CGH   Sean Davis
  • [BioC] array CGH   Hilmar Berger
• [BioC] help with ath1121501   Martin Olivier
  • [BioC] help with ath1121501   James W. MacDonald
  • [BioC] help with ath1121501   Seth Falcon
• [BioC] hs133phsentrezg metadata   James W. MacDonald
• [BioC] help with ath1121501   John Zhang
• [BioC] A question about reading FACS files using the rflowcyt package   Johan Lindberg
• [BioC] hs133phsentrezg metadata   De Bondt, An-7114 [PRDBE]
• [BioC] 3 factors with Limma.   Sharon
• [BioC] Normalisation GCRMA Error   Nicolas Servant
  • [BioC] Normalisation GCRMA Error   Ben Bolstad
    • [BioC] resolveMaps removed from AnnBuilder?   Wittner, Ben, Ph.D.
      • [BioC] resolveMaps removed from AnnBuilder?   James W. MacDonald
      • [BioC] resolveMaps removed from AnnBuilder?   Nianhua Li
• [BioC] Simple affymetrix question (treated vs non-treated)   Wonjong Moon
  • [BioC] Simple affymetrix question (treated vs non-treated)   James W. MacDonald
• [BioC] Spatial Correction   Justin Borevitz
  • [BioC] Spatial Correction   Matthew Lyon
• [BioC] Spatial Correction   Matthew Lyon
  • [BioC] Spatial Correction   Matthew Lyon
• [BioC] ECCB 06: Call for Late-Breaking Results   Hershel Safer
• [BioC] hs133phsentrezg metadata   Manhong Dai
  • [BioC] hs133phsentrezg metadata   James W. MacDonald
    • [BioC] hs133phsentrezg metadata   Manhong Dai
      • [BioC] hs133phsentrezg metadata   James W. MacDonald
      • [BioC] hs133phsentrezg metadata   Manhong Dai
      • [BioC] hs133phsentrezg metadata   Nianhua Li
• [BioC] Illumina Data transformation and Normalization   Simon Lin
• [BioC] aCGH and Affymetrix   Di Wu
  • [BioC] aCGH and Affymetrix   Sean Davis
• [BioC] Using GO functions without using LocusLink mappings   Khan, Anar
  • [BioC] Using GO functions without using LocusLink mappings   Seth Falcon
• [BioC] A question on GO annotations   Narinder Singh Sahni
  • [BioC] A question on GO annotations   Sean Davis
  • [BioC] A question on GO annotations   Oosting, J. (PATH)
• [BioC] syncLocalLibList in BioC 1.8 reposTools   Kimpel, Mark William
  • [BioC] syncLocalLibList in BioC 1.8 reposTools   Seth Falcon
• [BioC] ciona cdf environment   Karen Vranizan
• [BioC] aCGH and Affymetrix   Di Wu
• [BioC] problem with hyperGTest and ath1121501?   Martin Olivier
  • [BioC] problem with hyperGTest and ath1121501?   Seth Falcon
    • [BioC] straight t vs. bonferroni vs. all the new stuff.   Matthew Lyon
      • [BioC] straight t vs. bonferroni vs. all the new stuff.   Sean Davis
      • [BioC] straight t vs. bonferroni vs. all the new stuff.   Matthew Lyon
      • [BioC] straight t vs. bonferroni vs. all the new stuff.   Naomi Altman
      • [BioC] straight t vs. bonferroni vs. all the new stuff.   Matthew Lyon
      • [BioC] straight t vs. bonferroni vs. all the new stuff.   Sean Davis
    • [BioC] problem with hyperGTest and ath1121501?   Seth Falcon
• [BioC] How to use snapCGH with Nimblegen data   Romain Desprat
  • [BioC] How to use snapCGH with Nimblegen data   Steven McKinney
• [BioC] problem with hyperGTest and ath1121501?   Nianhua Li
• [BioC] beadarray example data problem   Keith Satterley
  • [BioC] beadarray example data problem   Mark Dunning
  • [BioC] beadarray example data problem 2   Keith Satterley
    • [BioC] beadarray example data problem 2   Martin Morgan
      • [BioC] beadarray example data problem 2   Keith Satterley
      • [BioC] beadarray example data problem 2   Mark Dunning
      • [BioC] beadarray example data problem 2   Martin Morgan
• [BioC] Designing a model matrix in limma for 4 conditions x 2 colors   Matthew Vaughn
• [BioC] How to adjust the power.t.test R function to reflect different experimental designs?   Nadia Messerschmidt
  • [BioC] How to adjust the power.t.test R function to reflect different experimental designs?   Davis, Sean (NIH/NCI) [E]
  • [BioC] How to adjust the power.t.test R function to reflect different experimental designs?   Naomi Altman
• [BioC] qqplot: theoretical Quantiles   Mohammad Esad-Djou
• [BioC] qqplot: theoretical Quantiles   shahrgol at web.de
  • [BioC] qqplot: theoretical Quantiles   Naomi Altman
    • [BioC] qqplot: theoretical Quantiles   stefano iacus
• [BioC] OFF TOPIC How measures is more appropriated to statistical analysis?   Marcelo Luiz de Laia
• [BioC] missing values limma question   lee
• [BioC] sensitivity of maxT correction   A S
• [BioC] Downloading data only once when building many annotation packages with AnnBuilder   David Weiss
  • [BioC] Downloading data only once when building many annotation packages with AnnBuilder   Nianhua Li
• [BioC] Using aggregators   Craddock, Richard C. (CDC/CCID/NCZVED) (CTR)
  • [BioC] Using aggregators   Martin Morgan
• [BioC] Affy probeset annotations   Karen Vranizan
  • [BioC] Affy probeset annotations   Kasper Daniel Hansen
  • [BioC] Affy probeset annotations   Nianhua Li
• [BioC] Assistance: mouse4302cdf installation   Alexander E. Lipka
• [BioC] job ad: position in UCSF Biostatistics   Fridlyand, Jane
• [BioC] Assistance: mouse4302cdf installation   Melissa Paczkowski
  • [BioC] Assistance: mouse4302cdf installation   lidaof
  • [BioC] Assistance: mouse4302cdf installation   lidaof
    • [BioC] Assistance: mouse4302cdf installation   Kasper Daniel Hansen
    • [BioC] Assistance: mouse4302cdf installation   Sean Davis
  • [BioC] Assistance: mouse4302cdf installation   James W. MacDonald
    • [BioC] Assistance: mouse4302cdf installation   lidaof
• [BioC] Lodplot problem   Daniel Brewer
  • [BioC] Lodplot problem   Oosting, J. (PATH)
• [BioC] lmFit(eset,design) error message   Benjamin Otto
  • [BioC] lmFit(eset,design) error message   James W. MacDonald
    • [BioC] lmFit(eset,design) error message   Benjamin Otto
• [BioC] gcrma on PM-only Affy data   Karen Vranizan
  • [BioC] gcrma on PM-only Affy data   Zhijin (Jean) Wu
• [BioC] SAM question (how to calculate the fudge term s0)   James Anderson
• [BioC] problems reading Illumina files using BeadExplorer   Vitalina Komashko
• [BioC] advice on absent present filtering needed   Kimpel, Mark William
  • [BioC] advice on absent present filtering needed   James W. MacDonald
  • [BioC] advice on absent present filtering needed   Naomi Altman
    • [BioC] advice on absent present filtering needed   Jenny Drnevich
      • [BioC] advice on absent present filtering needed   Kimpel, Mark William
      • [BioC] advice on absent present filtering needed   Sharon
• [BioC] Mirror configuration to install from local files with getBioC/biocLite   Thierry Sengstag
  • [BioC] Mirror configuration to install from local files with getBioC/biocLite   lidaof
• [BioC] ExpressionSet object to lmFit   Gordon Smyth
• [BioC] R plug-ins for Genespring   Margaret Gardiner-Garden
• [BioC] Mirror configuration to install from local files with getBioC/biocLite   lidaof
• [BioC] biomaRt: retrieve total chromosome lengths   De Bondt, An-7114 [PRDBE]
  • [BioC] biomaRt: retrieve total chromosome lengths   James W. MacDonald
    • [BioC] biomaRt: retrieve total chromosome lengths   Steffen Durinck
• [BioC] signals from different cell types   Lewin Eisele
• [BioC] Computing a diference of 2 differences from a CpG Island experiment using LimmaGUI   Richard Friedman
  • [BioC] Computing a diference of 2 differences from a CpG Island experiment using LimmaGUI   Darlene Goldstein
• [BioC] Create a vector of individual probes to remove from a CDF file   Dana Wohlbach
  • [BioC] Create a vector of individual probes to remove from a CDF file   Jenny Drnevich
• [BioC] [Bioc-devel] I will succeed (hopefully) the installation of Bioconductor 2.0   Francois Pepin
• [BioC] Is GNF1H gene chip package available   Srinivasan Ramachandran
• [BioC] Computing Copy Number from Affy 500K SNP Chips   Nicholas D. Socci
  • [BioC] Computing Copy Number from Affy 500K SNP Chips   Wittner, Ben, Ph.D.
• [BioC] Creating a .Rprofile   Melissa Paczkowski
  • [BioC] Creating a .Rprofile   Gregor Gorjanc
  • [BioC] Creating a .Rprofile   Sean Davis
• [BioC] RBGL compile error   YGC
  • [BioC] RBGL compile error   Li.Long at isb-sib.ch
• [BioC] Bioconductor Digest, Vol 44, Issue 28   Manhong Dai
  • [BioC] Bioconductor Digest, Vol 44, Issue 28   michael watson (IAH-C)
    • [BioC] Bioconductor Digest, Vol 44, Issue 28   Jenny Drnevich
• [BioC] 2 questions on Normalzation with LIMMAGUI   Richard Friedman
• [BioC] Microarray analysis and limma   john seers (IFR)
• [BioC] problems with Affy vignette and affybatch objects   Jenny Drnevich
  • [BioC] problems with Affy vignette and affybatch objects   James W. MacDonald
  • [BioC] problems with Affy vignette and affybatch objects   Seth Falcon
  • [BioC] problems with Affy vignette and affybatch objects   Martin Morgan
    • [BioC] problems with Affy vignette and affybatch objects   Jenny Drnevich
• [BioC] Golub (1999) Esets   McGee, Monnie
• [BioC] biomaRt: retrieve total chromosome lengths   De Bondt, An-7114 [PRDBE]
  • [BioC] biomaRt: retrieve total chromosome lengths   Sean Davis
    • [BioC] biomaRt: retrieve total chromosome lengths   Robert Gentleman
• [BioC] F-test vs.T-test-on-differences   Benjamin Otto
  • [BioC] F-test vs.T-test-on-differences   Naomi Altman
• [BioC] Nci-60 gene expression correlation coefficients   John Morrow

Last message date: Tue Oct 31 19:20:12 CET 2006
Archived on: Wed Nov 1 00:01:55 CET 2006

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