February 2004 Archives by thread

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Starting: Sun Feb 1 08:03:24 MEST 2004
Ending: Sun Feb 29 23:41:22 MEST 2004
Messages: 255

• [BioC] qc.stats error with mgu74av2   Dick Beyer
• [BioC] Normalization with cDNA array, Bioconductor Digest, Vol 11, Issue 44   Christopher Wilkinson
• [BioC] qc.stats error with mgu74av2   Crispin Miller
• [BioC] Limma: reading in additional spot data (flags)   Gordon K Smyth
• [BioC] normalize.quantiles generating incorrect output   Wolfgang Huber
• [BioC] bug in limma?   Gordon K Smyth
• [BioC] Re: Just a quick question   Gordon K Smyth
• [BioC] bug in limma?   Simon Melov
• [BioC] qc.stats error with mgu74av2   Crispin Miller
• [BioC] read.maimages   Jason Skelton
  • [BioC] read.maimages   Gordon Smyth
• [BioC] qc.stats error with mgu74av2   Crispin Miller
• [BioC] how do I add pheno data after making AffyBatch object   Hao Liu
  • [BioC] how do I add pheno data after making AffyBatch object   Rafael A. Irizarry
    • [BioC] how do I add pheno data after making AffyBatch object   Hao Liu
    • [BioC] get exprs from AffyBatch   Hao Liu
• [BioC] [limma] heatDiagram function doubts   Marcelo Luiz de Laia
• [BioC] how do I add pheno data after making AffyBatch object   James MacDonald
• [BioC] get exprs from AffyBatch   James MacDonald
  • [BioC] get exprs from AffyBatch   Rafael A. Irizarry
    • [BioC] get exprs from AffyBatch   Hao Liu
• [BioC] find and replace, average of 4 rows   Dr Gyorffy Balazs
• [BioC] t test   Binita Dutta
• [BioC] unbalanced factorial design   Christian Landry
  • [BioC] unbalanced factorial design   Kenny Ye
    • [BioC] unbalanced factorial design   Vincent Carey 525-2265
      • [BioC] unbalanced factorial design   Naomi Altman
      • [BioC] unbalanced factorial design   Francois Collin
      • [BioC] unbalanced factorial design   Kenny Ye
      • [BioC] unbalanced factorial design   Naomi Altman
      • [BioC] unbalanced factorial design   Douglas Bates
• [BioC] XML installation   Roger Vallejo
  • [BioC] XML installation   A.J. Rossini
  • [BioC] XML installation   Kasper Daniel Hansen
• [BioC] help loading libraries   Roger Vallejo
• [BioC] prooblem with replications   zhao luo
• [BioC] Development of GCRMA-like methods   Matthew Hannah
  • [BioC] Development of GCRMA-like methods   Rafael A. Irizarry
    • [BioC] Development of GCRMA-like methods   Richard Finney
      • [BioC] Development of GCRMA-like methods   Rafael A. Irizarry
• [BioC] Development of GCRMA-like methods   Matthew Hannah
• [BioC] Probeset   ABIGAIL ANN SCOTT
• [BioC] package "moe430acdf"   Roger Vallejo
  • [BioC] package "moe430acdf"   Jeff Gentry
• [BioC] error in annaffy   marlena.maziarz at utoronto.ca
• [BioC] newbie question: how do I get affy annotations   Hao Liu
  • [BioC] imageplot problem from limma   Anna Cao
    • [BioC] imageplot problem from limma   Gordon K Smyth
  • [BioC] newbie question: how do I get affy annotations   Johannes Freudenberg
• [BioC] GCRMA methods   Anthony Bosco
  • [BioC] GCRMA methods   Rafael A. Irizarry
• [BioC] mas5calls now almost like affymetrix's   Rafael A. Irizarry
• [BioC] question about limma fit differences?   Simon Melov
  • [BioC] question about limma fit differences?   Gordon Smyth
• [BioC] Development of GCRMA-like methods   Matthew Hannah
• [BioC] t test   Binita Dutta
• [BioC] makeProbePackage problems?   Matthew Hannah
• [BioC] newbie question: how do I get affy annotations   John Zhang
• [BioC] Different Normalizations   Julia Engelmann
  • [BioC] Different Normalizations   Susan Holmes
• [BioC] mas5calls now almost like affymetrix's   Tom R. Fahland
• [BioC] mas5calls now almost like affymetrix's   James MacDonald
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Digestion plot   Harry Hurd
• [BioC] Different Normalizations   Anja von Heydebreck
  • [BioC] Different Normalizations   Rafael A. Irizarry
    • [BioC] Different Normalizations   Anja von Heydebreck
      • [BioC] Program in R   E Motakis, Mathematics
      • [BioC] Program in R   Kenny Ye
      • [BioC] Program in R   Wolfgang Huber
• [BioC] Question about the correct usage of the lme() function (from the nlme package).   Alex F. Bokov
• [BioC] Dye swap time course experiment in marrayinput   Naomi Altman
• [BioC] Digestion plot   Rich Haney
• [BioC] question about housekeeping gene   zhao luo
  • [BioC] question about housekeeping gene   Pete Lee
• [BioC] question about 'Outliers (bad spots) are handled with replication'   zhao luo
• [BioC] Re: Limma: four suggestions related to weights and background correction   Gordon Smyth
  • [BioC] Re: Limma: four suggestions related to weights and background correction   Ramon Diaz-Uriarte
    • [BioC] Re: Limma: four suggestions related to weights and background correction   Gordon Smyth
      • [BioC] Re: Limma: four suggestions related to weights and background correction   Ramon Diaz-Uriarte
• [BioC] Signal to noise   Caroline TRUNTZER
• [BioC] Re: Bioconductor Digest, Vol 12, Issue 10   Tarca Adi Laurentiu
• [BioC] Print-tip Normalization of dye swap experiments using marrayNorm   Richard Friedman
• [BioC] M vs A plot   Richard Friedman
• [BioC] Papers mentioning duplicate spots   Gordon Smyth
• [BioC] M vs A plot   Richard Friedman
  • [BioC] M vs A plot   Wolfgang Huber
    • [BioC] M vs A plot   Richard Friedman
      • [BioC] M vs A plot   Wolfgang Huber
• [BioC] Re: remlscore function / random effects   Gordon Smyth
• [BioC] Position Available. Genomics Core   Michael McClelland
• [BioC] Papers mentioning duplicate spots   Oliver Hartmann
  • [BioC] Papers mentioning duplicate spots   Wolfgang Huber
    • [BioC] Papers mentioning duplicate spots   Wolfgang Huber
• [BioC] Re: FW: makeProbePackage problems?   Wolfgang Huber
• [BioC] Re: FW: makeProbePackage problems?   James MacDonald
• [BioC] Re: FW: makeProbePackage problems?   Matthew Hannah
• [BioC] widgetTools library, checkButton function   Tom Price
• [BioC] widgetTools library, checkButton function   John Zhang
• [BioC] Is it okay to do 2 loess normalizations in a row?   Richard Friedman
• [BioC] Edit sample Names   Yen Lin Chia
• [BioC] warning message from using gcrma   Caimiao Wei
  • [BioC] warning message from using gcrma   Rafael A. Irizarry
• [BioC] Subtraction with NA values   Daniel F. Simola
  • [BioC] Subtraction with NA values   A.J. Rossini
    • [BioC] Subtraction with NA values   Gordon Smyth
      • [BioC] Subtraction with NA values   A.J. Rossini
      • [BioC] Subtraction with NA values   Gordon Smyth
• [BioC] Quantile Normalization on mice data   Yen Lin Chia
• [BioC] Quantile normalization, tail correction?   Yen Lin Chia
• [BioC] Layout in limma   Binita Dutta
  • [BioC] Layout in limma   Gordon Smyth
• [BioC] GCRMA missing value error on ATH1 chip   Matthew Hannah
  • [BioC] GCRMA missing value error on ATH1 chip   Zhijin Wu
• [BioC] about the use of maW in marrayInput   Margherita
• [BioC] downloading Bioconductor   Pamela Wolfe
  • [BioC] downloading Bioconductor   Jeff Gentry
• [BioC] widgetTools library, checkButton function   John Zhang
• [BioC] exporting data from limma and among slide normalization   Christian Landry
  • [BioC] exporting data from limma and among slide normalization   Gordon Smyth
• [BioC] RMA   Hua Li
• [BioC] Edit sample Names   James MacDonald
  • [BioC] Edit sample Names   Aedin
• [BioC] Edit sample Names   James MacDonald
  • [BioC] Edit sample Names   Aedin
• [BioC] Limma and Affymetrix ?   Stan Smiley
• [BioC] AffyPLM   Yen Lin Chia
  • [BioC] AffyPLM   Ben Bolstad
• [BioC] question about 'Outliers (bad spots) are handled with replication'   zhao luo
• [BioC] calcuate the expression values with AFFX-xxx Genes   Linlin Chen
• [BioC] loading bioconductor   Hanna Craig
  • [BioC] loading bioconductor   Jeff Gentry
• [BioC] justRMA() execution problems   Srikanth
• [BioC] justRMA() execution problems   James MacDonald
• [BioC] ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)   Matthew Hannah
• [BioC] ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)   Matthew Hannah
• [BioC] ath1121501probe_1.0 error (was GCRMA missing value error)   Matthew Hannah
• [BioC] ath1121501probe_1.0 error (was GCRMA missing value error)   James MacDonald
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Papers mentioning duplicate spots   Martin Enge
• [BioC] ath1121501probe_1.0 error (was GCRMA missing value error)   Matthew Hannah
  • [BioC] ath1121501probe_1.0 error (was GCRMA missing value error)   Jeff Gentry
• [BioC] M vs A plot   Naomi Altman
  • [BioC] M vs A plot   Richard Friedman
• [BioC] MvA plot   Martino Barenco
  • [BioC] MvA plot   Elisabetta Manduchi
  • [BioC] MvA plot   Jean Yee Hwa Yang
    • [BioC] MvA plot   Rafael A. Irizarry
  • [BioC] MvA plot   Rich Haney
• [BioC] MvA plot   Gordon Smyth
• [BioC] Statistical comparison of low replicate affy data   Matthew Hannah
  • [BioC] Statistical comparison of low replicate affy data   Rafael A. Irizarry
• [BioC] wee query on pamr.knnimpute   Aedin
• [BioC] Statistical comparison of low replicate affy data   Matthew Hannah
  • [BioC] AffyPLM   Lawrence Paul Petalidis
    • [BioC] AffyPLM   Francois Collin
      • [BioC] AffyPLM   Naomi Altman
• [BioC] Statistical comparison of low replicate affy data   James MacDonald
• [BioC] marrayClasses packages   Gu, Joyce
• [BioC] (no subject)   Joyce Gu
  • [BioC] (no subject)   Jean Yee Hwa Yang
• [BioC] Mising data   Joyce Gu
  • [BioC] Mising data   Jean Yee Hwa Yang
• [BioC] Segfault in affy:rma() with custom chip   Warnes, Gregory R
• [BioC] raw intensities in affymetrix .cel files   YUK FAI LEUNG
• [BioC] Statistical comparison of low replicate affy data   Matthew Hannah
• [BioC] limma 1.3.4 for Win   Stephen Henderson
  • [BioC] limma 1.3.4 for Win   Gordon Smyth
• [BioC] raw intensities in affymetrix .cel files   James MacDonald
• [BioC] AffyPLM   Matthew Hannah
• [BioC] RAqua installation problem   Ann Loraine
• [BioC] Re: Bioconductor Digest, Vol 12, Issue 28   Tarca Adi Laurentiu
• [BioC] Mising data   Alex F. Bokov
• [BioC] (no subject)   Joyce Gu
• [BioC] Segfault in affy:rma() with custom chip   Warnes, Gregory R
• [BioC] Re: raw intensities in affymetrix .cel files   YUK FAI LEUNG
• [BioC] (no subject)   Jamila Ahdidan
• [BioC] Re: marrayClasses algorithm   Jean Yee Hwa Yang
• [BioC] limma 1.5.1 ok under R 1.8 or R 1.9   Gordon Smyth
• [BioC] marray or rma?   gjam at daimi.au.dk
  • [BioC] marray or rma?   Adaikalavan Ramasamy
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] marray or rma?   James MacDonald
• [BioC] Question about excluding Affymetrix spike controls from normalization   Tan, MinHan
• [BioC] problem with LPE   Phguardiol at aol.com
  • [BioC] Re: problem with LPE   Nitin Jain
• [BioC] Overriding maPrintTip method   Kellie J. Archer, Ph.D.
• [BioC] limma   Anna Cao
• [BioC] rma or svn?   gjam at daimi.au.dk
  • [BioC] rma or svn?   Rafael A. Irizarry
• [BioC] testing GO categories with Fisher's exact test.   Nicholas Lewin-Koh
  • [BioC] Re: testing GO categories with Fisher's exact test.   Ramon Diaz-Uriarte
    • [BioC] Re: testing GO categories with Fisher's exact test.   Madhuchhanda Bhattacharjee
  • [BioC] testing GO categories with Fisher's exact test.   cberry at tajo.ucsd.edu
• [BioC] testing GO categories with Fisher's exact test.   Arne.Muller at aventis.com
• [BioC] testing GO categories with Fisher's exact test.   michael watson (IAH-C)
• [BioC] testing GO categories with Fisher's exact test.   Arne.Muller at aventis.com
• [BioC] problems with multtest   michael watson (IAH-C)
  • [BioC] Reading data from SMD database   Aedin
  • [BioC] problems with multtest   Marcel Dettling
• [BioC] problems with multtest   Stephen Henderson
• [BioC] Questions about multtest   michael watson (IAH-C)
• [BioC] problems with multtest   James MacDonald
• [BioC] Questions about multtest   Sean Davis
• [BioC] Questions about multtest   Oosting, J. (PATH)
  • [BioC] Questions about multtest   Rafael A. Irizarry
• [BioC] Reading data from SMD database   Colin Smith
  • [BioC] Reading data from SMD database   Aedin
• [BioC] M vs A plot   Naomi Altman
• [BioC] testing GO categories with Fisher's exact test.   michael watson (IAH-C)
  • [BioC] testing GO categories with Fisher's exact test.   Ramon Diaz-Uriarte
    • [BioC] testing GO categories with Fisher's exact test.   Nicholas Lewin-Koh
• [BioC] testing GO categories with Fisher's exact test.   Arne.Muller at aventis.com
• [BioC] testing GO categories with Fisher's exact test.   James MacDonald
  • [BioC] testing GO categories with Fisher's exact test.   Ramon Diaz-Uriarte
    • [BioC] error when running marrayNorm   Yihuan Xu
      • [BioC] error when running marrayNorm   Jean Yee Hwa Yang
      • [BioC] error when running marrayNorm   Yihuan Xu
      • [BioC] error when running marrayNorm   Jean Yee Hwa Yang
• [BioC] cDNA microarray Questions   rwin qian
  • [BioC] cDNA microarray Questions   Aedin
• [BioC] limma: merging RG list and normalisation   Christopher Wilkinson
  • [BioC] limma: merging RG list and normalisation   Gordon Smyth
• [BioC] normalization   gjam at daimi.au.dk
• [BioC] normalization   Arne.Muller at aventis.com
• [BioC] affyPLM interpretation   Arne.Muller at aventis.com
• [BioC] LimmaGUI   Binita Dutta
• [BioC] LimmaGUI   James MacDonald
• [BioC] E.coli CDF   Ilhem Diboun
• [BioC] Bioconductor Macintosh Package bundle   don simone daly
• [BioC] Limma Package to read cDNA data   Joyce Gu
  • [BioC] Limma Package to read cDNA data   Matthew Ritchie
• [BioC] (no subject)   Wenqiong Chen
  • [BioC] (no subject)   Gordon K Smyth
• [BioC] gcrma error   Anthony Bosco
  • [BioC] gcrma error   Rafael A. Irizarry
• [BioC] Error when calculating coverageMat in ontoTools 1.2.1   Rohan BH Williams
• [BioC] error when running marrayNorm   michael watson (IAH-C)
• [BioC] cDNA microarray Questions   michael watson (IAH-C)
  • [BioC] cDNA microarray Questions   Naomi Altman
• [BioC] E.coli CDF (fwd)   Caroline Johnston
• [BioC] normalization   gjam at daimi.au.dk
• [BioC] limma package and related replicate genes problems   p hu
  • [BioC] limma package and related replicate genes problems   Matthew Ritchie
• [BioC] (no subject)   James MacDonald
• [BioC] Re: Evaluate correlation beween biological replicates   Hua Weng
• [BioC] limma design matrix   michael watson (IAH-C)
• [BioC] An ESR essay about software design, and how it applies to Bioconductor   Alex F. Bokov
  • [BioC] An ESR essay about software design, and how it applies to Bioconductor   A.J. Rossini
  • [BioC] An ESR essay about software design, and how it applies to Bioconductor   Vincent Carey 525-2265
    • [BioC] An ESR essay about software design, and how it applies to Bioconductor   Naomi Altman
• [BioC] problem with ttestFun   Naomi Altman
• [BioC] Recent changes to Bioconductor packages   madman at jimmy.harvard.edu
• [BioC] Intensity distribution of "significant genes"   Naomi Altman
• [BioC] installing affy devel package   Isaac Mehl

Last message date: Sun Feb 29 23:41:22 MEST 2004
Archived on: Mon Mar 1 15:59:16 MEST 2004

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