December 2005 Archives by thread

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Starting: Thu Dec 1 00:25:50 CEST 2005
Ending: Sat Dec 31 15:59:30 CEST 2005
Messages: 281

• [BioC] double-logging in MAplot(abatch, pairs=T)   Jenny Drnevich
  • [BioC] double-logging in MAplot(abatch, pairs=T)   Ben Bolstad
• [BioC] Working with low abundance probesets !!   Sharon Anbu
• [BioC] Research Associate in Applied Statistical Bioinformatics - Oxford University   Steve Taylor
  • [BioC] Associate Scientist I/II position in biomarker group at MedImmune Inc.   yihong yao
• [BioC] Working with low abundance probesets !!   Sharon Anbu
  • [BioC] Working with low abundance probesets !!   Sean Davis
    • [BioC] Working with low abundance probesets !!   Sharon Anbu
      • [BioC] three group ANOVA   kfbargad at ehu.es
• [BioC] How to validate normalization?   krasikov at science.uva.nl
• [BioC] merging fit and MA objects   Ido M. Tamir
• [BioC] merging fit and MA objects   Ido M. Tamir
• [BioC] Affy autodownload cdf problem   Seth Falcon
• [BioC] Re-scaling MA plot Y axis in LimmaGUI?   J.delasHeras at ed.ac.uk
• [BioC] Masking single Oligos in mas5   Benjamin Otto
  • [BioC] Masking single Oligos in mas5   Ariel Chernomoretz
    • [BioC] Masking single Oligos in mas5   Benjamin Otto
      • [BioC] Masking single Oligos in mas5   Benjamin Otto
      • [BioC] [SPAM???] Re: Masking single Oligos in mas5   Ariel Chernomoretz
      • [BioC] [SPAM???] Re: Masking single Oligos in mas5   Benjamin Otto
      • [BioC] [SPAM???] Re: Masking single Oligos in mas5   Ariel Chernomoretz
      • [BioC] [SPAM???] Re: Masking single Oligos in mas5   Benjamin Otto
      • [BioC] Final: Masking single Oligos in mas5   Benjamin Otto
  • [BioC] Masking single Oligos in mas5   Jenny Drnevich
• [BioC] limma: eBayes / topTable and the choice of the "proportion" parameter for models with multiple contrasts   Dr. D. P. Kreil
  • [BioC] limma: eBayes / topTable and the choice of the "proportion" parameter for models with multiple contrasts   Dr. D. P. Kreil
  • [BioC] limma: eBayes / topTable and the choice of the "proportion" parameter for models with multiple contrasts   Gordon Smyth
• [BioC] gpr one color   kirk hammet
• [BioC] Re-scaling MA plot Y axis in LimmaGUI?   J.delasHeras at ed.ac.uk
• [BioC] limma: semi-bug (?) report for toptable   Dr. D. P. Kreil
• [BioC] gpr one color   Paquet, Agnes
  • [BioC] preprocessing one color   kirk hammet
• [BioC] one color   kirk hammet
• [BioC] bug in overview function of made4   Jenny Drnevich
  • [BioC] bug in overview function of made4   Seth Falcon
• [BioC] DB connection error   Michel JUGE
  • [BioC] DB connection error   sdurinck at ebi.ac.uk
• [BioC] How to validate normalization?   krasikov at science.uva.nl
• [BioC] BioC web-site   Arne.Muller at sanofi-aventis.com
  • [BioC] BioC web-site   Jeff Gentry
    • [BioC] BioC web-site   Giulio Di Giovanni
  • [BioC] BioC web-site   Seth Falcon
• [BioC] BioC web-site   Arne.Muller at sanofi-aventis.com
• [BioC] duplicateCorrelation   Hua Weng
  • [BioC] duplicateCorrelation   Gordon Smyth
• [BioC] bugs in arrayQuality and marray   Francois Pepin
• [BioC] bugs in arrayQuality and marray   Francois Pepin
• [BioC] bugs in arrayQuality and marray   Paquet, Agnes
• [BioC] normexp (limma) failure?   Gordon Smyth
• [BioC] Limma toptable question   Gordon Smyth
• [BioC] limma: semi-bug (?) report for toptable   Gordon Smyth
• [BioC] Database for Microarray Data - request for user stories   Ido M. Tamir
  • [BioC] Database for Microarray Data - request for user stories   David Ruau
    • [BioC] Database for Microarray Data - request for user stories   Henrik Bengtsson
  • [BioC] Database for Microarray Data - request for user stories   jon butchar
• [BioC] Biobase/affy installation problem in linux   Frank Duan
• [BioC] Biobase/affy installation problem in linux   Frank Duan
  • [BioC] Biobase/affy installation problem in linux   Benilton Carvalho
    • [BioC] Biobase/affy installation problem in linux   Frank Duan
    • [BioC] Biobase/affy installation problem in linux   Frank Duan
• [BioC] Database for Microarray Data - request for user stories   James MacDonald
• [BioC] From KEGG pathways to Affy ProbeID   Sharon Anbu
  • [BioC] From KEGG pathways to Affy ProbeID   Andrej Kastrin
• [BioC] From KEGG pathways to Affy ProbeID   John Zhang
  • [BioC] Match the probe sets from three microarray platforms   weinong han
    • [BioC] Match the probe sets from three microarray platforms   Sean Davis
• [BioC] bug in overview function of made4   Aedin Culhane
• [BioC] ANN: Advanced R programming course, Seattle in Jan   Seth Falcon
• [BioC] (Limma) different toptable results for the same dataset using 2 different designs   Celine Carret
• [BioC] custom PM only chips and CDF files   Stephen Henderson
  • [BioC] custom PM only chips and CDF files   Kasper Daniel Hansen
    • [BioC] custom PM only chips and CDF files   Ben Bolstad
      • [BioC] custom PM only chips and CDF files   Kasper Daniel Hansen
  • [BioC] custom PM only chips and CDF files   Celine Carret
• [BioC] bugs in arrayQuality and marray   Paquet, Agnes
• [BioC] custom PM only chips and CDF files   Stephen Henderson
• [BioC] decideTests nestedF   daniela marconi
• [BioC] three group ANOVA   Gordon K Smyth
• [BioC] (Limma) different toptable results for the same dataset using 2 different designs   Gordon K Smyth
  • [BioC] (Limma) different toptable results for the same dataset using 2 different designs   Celine Carret
    • [BioC] (Limma) different toptable results for the same dataset using 2 different designs   Gordon Smyth
• [BioC] error using R   S B
  • [BioC] Single-Channel Normalization using Bioconductor   Paul Lang
    • [BioC] Single-Channel Normalization using Bioconductor   Wolfgang Huber
• [BioC] Debian Sarge   kirk hammet
  • [BioC] Debian Sarge   Marcelo Luiz de Laia
• [BioC] Fwd:decideTests nestedF   daniela marconi
• [BioC] Bioconductor Digest, Vol 34, Issue 5   Wu, Xiwei
  • [BioC] Bioconductor Digest, Vol 34, Issue 5   Michel JUGE
• [BioC] Debian Sarge   Kort, Eric
• [BioC] Error message from R2.2.0 on Linux   Hua Weng
  • [BioC] Error message from R2.2.0 on Linux   Kasper Daniel Hansen
    • [BioC] Error message from R2.2.0 on Linux   Hua Weng
      • [BioC] Error message from R2.2.0 on Linux   Kasper Daniel Hansen
      • [BioC] Error message from R2.2.0 on Linux   Hua Weng
      • [BioC] Error message from R2.2.0 on Linux   Kasper Daniel Hansen
      • [BioC] Error message from R2.2.0 on Linux   Kasper Daniel Hansen
      • [BioC] Error message from R2.2.0 on Linux   J.delasHeras at ed.ac.uk
• [BioC] Time course experiment   Khan, Sohail
  • [BioC] Time course experiment   kfbargad at ehu.es
    • [BioC] Time course experiment   Yu Chuan Tai
  • [BioC] Time course experiment   Naomi Altman
  • [BioC] Time course experiment   martabar at um.es
• [BioC] Rocke-Lorenzato model or Global Error Model in Bioconductor   Ruppert Valentino
  • [BioC] Rocke-Lorenzato model or Global Error Model in Bioconductor   Wolfgang Huber
  • [BioC] Rocke-Lorenzato model or Global Error Model in Bioconductor   Greg Finak
• [BioC] Error message from R2.2.0 on Linux   Gordon Smyth
  • [BioC] Error message from R2.2.0 on Linux   Hua Weng
• [BioC] How to perform the TukeyHSD test properly?   Groot, Philip de
• [BioC] AnnBuilder/ABPkgBuilder URL problem   Anja Schiel
  • [BioC] AnnBuilder/ABPkgBuilder URL problem   Ting-Yuan Liu
• [BioC] Limma: mean for M values   Ido M. Tamir
• [BioC] Evaluating differentiall expressed genes   Tim Smith
  • [BioC] Evaluating differentiall expressed genes   Sean Davis
    • [BioC] Evaluating differentiall expressed genes   Tim Smith
      • [BioC] Evaluating differentiall expressed genes   Naomi Altman
      • [BioC] Evaluating differentiall expressed genes   Seth Falcon
      • [BioC] Evaluating differentiall expressed genes   Naomi Altman
      • [BioC] Evaluating differentiall expressed genes   Kasper Daniel Hansen
      • [BioC] Evaluating differentiall expressed genes   Holger Schwender
• [BioC] multtest/mt.teststat t with equal or unequal variances   Ann Hess
• [BioC] affycomp   kirk hammet
• [BioC] kOverA function   Lana Schaffer
• [BioC] kOverA understood   Lana Schaffer
  • [BioC] extracting top120 genes after SAM analysis   Gregor Siegler
• [BioC] Single-Channel Normalization using Bioconductor   Gordon Smyth
• [BioC] need a neural network package for microarray data analysis   madhurima bhattacharjee
• [BioC] need a neural network package for microarray data analysis   Stephen Henderson
• [BioC] Limma vs Maanova, and use of covariates   Ingunn Berget
  • [BioC] Limma vs Maanova, and use of covariates   Naomi Altman
  • [BioC] Limma vs Maanova, and use of covariates   Juan Pedro Steibel
    • [BioC] Limma vs Maanova, and use of covariates   Ingunn Berget
• [BioC] Limma: Calculating the interaction term in a 3x2 factorial design with two colour microarrays!   michael watson (IAH-C)
• [BioC] need a neural network package for microarray data   Tarca, Adi
• [BioC] PLIER Tech Note   Lelivelt, Mike
• [BioC] Limma and creating design matrices for complex loop designs   michael watson (IAH-C)
  • [BioC] Limma and creating design matrices for complex loop designs   Naomi Altman
• [BioC] Limma and creating design matrices for complex loop designs   Naomi Altman
• [BioC] Limma and creating design matrices for complex loop designs   Gordon Smyth
• [BioC] how to use R read CHP file   zhu zhidong
• [BioC] how to use R read CHP file   zhu zhidong
  • [BioC] how to use R read CHP file   Kasper Daniel Hansen
    • [BioC] how to use R read CHP file   Ben Bolstad
      • [BioC] how to use R read CHP file   Kasper Daniel Hansen
• [BioC] Limma and creating design matrices for complex loop designs   michael watson (IAH-C)
  • [BioC] Limma and creating design matrices for complex loop designs   Gordon Smyth
• [BioC] hgu133aMAP2PROBE...?   Dario Greco
  • [BioC] hgu133aMAP2PROBE...?   Furge, Kyle
  • [BioC] hgu133aMAP2PROBE...?   Ting-Yuan Liu
• [BioC] LIMMA:nestedF in   Daniela Marconi
• [BioC] LIMMA:nestedF   daniela marconi
• [BioC] Rocke-Lorenzato model or Global Error Model in Bioconductor   Norman Pavelka
• [BioC] hgu133aMAP2PROBE...?   John Zhang
• [BioC] rbind in annaffy problem   Kimpel, Mark William
  • [BioC] rbind in annaffy problem   James W. MacDonald
• [BioC] hgu133aMAP2PROBE...fixed!   Dario Greco
• [BioC] design question in Limma: double dye swap with replication   Ana Conesa
• [BioC] R from perl   madhurima bhattacharjee
  • [BioC] R from perl   Sean Davis
• [BioC] R from perl   Sean Davis
  • [BioC] R from perl   Steffen Durinck
    • [BioC] R from perl   Sean Davis
• [BioC] November BioC Devel Changelog   James MacDonald
  • [BioC] November BioC Devel Changelog   Seth Falcon
• [BioC] Displaying multiple survival curves on one graph   Rifat Hamoudi
  • [BioC] Displaying multiple survival curves on one graph   Seth Falcon
• [BioC] [LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4   Ron Ophir
• [BioC] Problem with RSPerl   madhurima bhattacharjee
  • [BioC] Problem with RSPerl   Seth Falcon
• [BioC] [LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4   Gordon K Smyth
• [BioC] problem with loading affyQCReport   Tuomas Raitila
  • [BioC] problem with loading affyQCReport   Seth Falcon
    • [BioC] problem with loading affyQCReport   Herve Pages
      • [BioC] can't get simpleaffy for Macs; was: Re: problem with loading affyQCReport   Jenny Drnevich
      • [BioC] can't get simpleaffy for Macs; was: Re: problem with loading affyQCReport   Herve Pages
• [BioC] R from perl   Kort, Eric
• [BioC] [R] [R-pkgs] New Quantian release with over 800 CRAN/BioC packages   Dirk Eddelbuettel
• [BioC] (no subject)   jg295 at mole.bio.cam.ac.uk
  • [BioC] (no subject)   Kort, Eric
• [BioC] R from Perl   Duncan Temple Lang
• [BioC] Problem with RSPerl   Duncan Temple Lang
• [BioC] IQR question   Jianping Jin
• [BioC] R/maanova   Gary Churchill
• [BioC] building a "for loop" with getGene, biomaRt   Morten Mattingsdal
  • [BioC] building a "for loop" with getGene, biomaRt   Sean Davis
  • [BioC] building a "for loop" with getGene, biomaRt   sdurinck at ebi.ac.uk
• [BioC] Affy: Increase/Decrease two sided Wilcoxons test   Benjamin Otto
• [BioC] Targets file, array labels and Limma versions   Jenny Drnevich
  • [BioC] Targets file, array labels and Limma versions   Marcus Davy
  • [BioC] Targets file, array labels and Limma versions   Gordon Smyth
    • [BioC] Targets file, array labels and Limma versions   Jenny Drnevich
• [BioC] how to use pData output to select columns from an exprset object?   Ochsner, Scott A
  • [BioC] how to use pData output to select columns from an exprsetobject?   kfbargad at ehu.es
• [BioC] limma - RG.MA   Naomi Altman
• [BioC] limma - RG.MA   Gordon K Smyth
  • [BioC] limma - RG.MA   Naomi Altman
• [BioC] [Rd] R for Windows GUI Front-End Problem (PR#3364)   Kasper Daniel Hansen
• [BioC] Data Frame Error in Affycomp   McGee, Monnie
• [BioC] (Limma) LmFit and fit object   Beatriz
• [BioC] AnnBuilder URL   Toni Julià
  • [BioC] AnnBuilder URL   Ting-Yuan Liu
• [BioC] srcUrl function in AnnBuilder   Shi, Tao
• [BioC] srcUrl function in AnnBuilder   Shi, Tao
  • [BioC] srcUrl function in AnnBuilder   Seth Falcon
  • [BioC] srcUrl function in AnnBuilder   Ting-Yuan Liu
    • [BioC] srcUrl function in AnnBuilder   Shi, Tao
• [BioC] missing function in duplicateCorrelation?   Jenny Drnevich
• [BioC] ".qcEnv not found"   Lana Schaffer
• [BioC] Data Frame Error in Affycomp   McGee, Monnie
• [BioC] need help in nnet   madhurima bhattacharjee
• [BioC] Rgraphviz: adding weight to an edge   Kaustubh Patil
  • [BioC] Rgraphviz: adding weight to an edge   Ting-Yuan Liu
  • [BioC] Rgraphviz: adding weight to an edge   Jeff Gentry
  • [BioC] Rgraphviz: adding weight to an edge   Wolfgang Huber
    • [BioC] Rgraphviz: adding weight to an edge   Kaustubh Patil
      • [BioC] Rgraphviz: adding weight to an edge   Jeff Gentry
      • [BioC] Rgraphviz: adding weight to an edge   Kaustubh Patil
• [BioC] Install Rmpi on Fedora with mpich2 installed.   Ye, Bin
  • [BioC] Install Rmpi on Fedora with mpich2 installed.   Li Long
    • [BioC] Install Rmpi on Fedora with mpich2 installed.   Ye, Bin
      • [BioC] Install Rmpi on Fedora with mpich2 installed.   Li Long
• [BioC] Time course experiment....   Khan, Sohail
• [BioC] Background corrected PM, MM intensities   Rad Nag
  • [BioC] Background corrected PM, MM intensities   James W. MacDonald
• [BioC] Using MAANOVA functions   Heather Maughan
  • [BioC] Using MAANOVA functions   James W. MacDonald
    • [BioC] Using MAANOVA functions   Wolfgang Huber
• [BioC] Limma Coefficients using lmscFit   Naomi Altman
  • [BioC] Cutoff selection for MassSpec   smohapat at vbi.vt.edu
• [BioC] nnet   madhurima bhattacharjee
• [BioC] Rgraphviz: adding weight to an edge   Jamain, Adrien J
  • [BioC] Rgraphviz: adding weight to an edge   Li Long
• [BioC] Rgraphviz: adding weight to an edge   Jamain, Adrien J
  • [BioC] Rgraphviz: adding weight to an edge   Li Long
• [BioC] need help in nnet (madhurima bhattacharjee)   Tarca, Adi
• [BioC] position in biostatistics - Lille France   Sophie Gallina
• [BioC] frustration with this interface   david clayton
  • [BioC] frustration with this interface   Robert Gentleman
• [BioC] Limma Coefficients using lmscFit   Gordon K Smyth
  • [BioC] Limma Coefficients using lmscFit   Sean Davis
    • [BioC] Limma Coefficients using lmscFit   Naomi Altman
• [BioC] how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help   Saurin Jani
  • [BioC] how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help   Sean Davis
    • [BioC] how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help   Naomi Altman
      • [BioC] how to get samoutput$mat.fdr,   Saurin Jani
    • [BioC] how to get samoutput$mat.fdr,   Saurin Jani
• [BioC] FAQs and e-mail archive   Naomi Altman
• [BioC] Rgraphviz: adding weight to an edge   Jeff Gentry
• [BioC] Retrieving microarray data from GEO?   Simon Lin
• [BioC] Retrieving microarray data from GEO?   John Zhang
• [BioC] Newbie question regarding SAM analysis   Ettinger, Nicholas
• [BioC] Using MAANOVA functions   Xiangqin Cui
  • [BioC] merging two sets of genes   kfbargad at ehu.es
    • [BioC] merging two sets of genes   Seth Falcon
      • [BioC] merging two sets of genes   Robert Gentleman
      • [BioC] merging two sets of genes   kfbargad at ehu.es
• [BioC] justRMA and custom CDF   Anthony Bosco
  • [BioC] justRMA and custom CDF   James W. MacDonald
• [BioC] Installing Bioconductor on a Rocks Cluster   Daniel Davidson
  • [BioC] Installing Bioconductor on a Rocks Cluster   Seth Falcon
• [BioC] Newbie question regarding SAM analysis   Simon Lin
• [BioC] Help with EBAM from siggenes   Ettinger, Nicholas
  • [BioC] Help with EBAM from siggenes   Holger Schwender
• [BioC] [Limma] annotation (probeids) and as.environment   Claudia Molina
  • [BioC] [Limma] annotation (probeids) and as.environment   Ting-Yuan Liu
    • [BioC] [Limma] annotation (probeids) and as.environment   Claudia Molina
• [BioC] Limma error - undefined columns selected   Ankit Pal
• [BioC] Help to Design my 'cl' file for use with SAM, EBAM, RankProd   Ettinger, Nicholas
• [BioC] merging two sets of genes   Robert Gentleman
  • [BioC] merging two sets of genes   kfbargad at ehu.es
  • [BioC] merging two sets of genes   kfbargad at ehu.es
    • [BioC] merging two sets of genes   Kasper Daniel Hansen
• [BioC] Limma then Annaffy?   davidl at unr.nevada.edu
  • [BioC] Limma then Annaffy?   Eric Kort
  • [BioC] Limma then Annaffy?   James W. MacDonald
    • [BioC] Limma then Annaffy? solved   davidl at unr.nevada.edu
• [BioC] Single slide analysis using Limma   Ankit Pal
  • [BioC] Single slide analysis using Limma   Sean Davis
  • [BioC] Single slide analysis using Limma   Naomi Altman
    • [BioC] Single slide analysis using Limma   Vincent Carey 525-2265
      • [BioC] Single slide analysis using Limma   Naomi Altman

Last message date: Sat Dec 31 15:59:30 CEST 2005
Archived on: Sat Dec 31 15:59:43 CEST 2005

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