January 2005 Archives by author

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Starting: Sat Jan 1 17:49:02 CEST 2005
Ending: Mon Jan 31 21:30:08 CEST 2005
Messages: 293

• [BioC] What is limma saying about my data?   michael watson (IAH-C)
• [BioC] Significant p-values disappear in limma   michael watson (IAH-C)
• [BioC] Significant p-values disappear in limma   michael watson (IAH-C)
• [BioC] Problems installing KEGGSOAP   michael watson (IAH-C)
• [BioC] Problems installing KEGGSOAP   michael watson (IAH-C)
• [BioC] Typo in KEGGSOAP 0.6.5?   michael watson (IAH-C)
• [BioC] KEGGSOAP - Error in xmlName(node[[1]]) : no applicable method for "xmlName"   michael watson (IAH-C)
• [BioC] problem with siggenes   michael watson (IAH-C)
• [BioC] search probe-ids for gene-symbols   Vincent Carey 525-2265
• [BioC] affy Yeast 2.0 annotation   Vincent Carey 525-2265
• [BioC] hgu133_plus_2?   Carl-Magnus Högerkorp
• [BioC] Searching for a cDNA spike-in data set that is public available   Peter Sørensen (HAG)
• [BioC] vsn in limma or marray/arrayMagic   A.E.Schiel at lumc.nl
• [BioC] vsn in limma or marray/arrayMagic   A.E.Schiel at lumc.nl
• [BioC] limma   A.E.Schiel at lumc.nl
• [BioC] A question about Limma   Naomi Altman
• [BioC] Significant p-values disappear in limma   Naomi Altman
• Re: [BioC] F-tests for factorial effects - limma   Naomi Altman
• [BioC] F-tests for factorial effects - limma   Naomi Altman
• [BioC] A question about Limma   Naomi Altman
• [BioC] limma design matrix   Naomi Altman
• [BioC] limma - FDR adjusted "p-values"   Naomi Altman
• [BioC] Dose-Response: Regressiion and ANOVA   Arne.Muller at aventis.com
• [BioC] GCRMA question   Arne.Muller at sanofi-aventis.com
• [BioC] hu6800 Data package   William Barry
• [BioC] Fw: random location of duplicate spots and use of limma   Ingunn Berget
• [BioC] Re: random location of duplicate spots and use of limma   Ingunn Berget
• [BioC] Limma, decideTests   Ingunn Berget
• [BioC] Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf   Dick Beyer
• [BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO   Dick Beyer
• [BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO   Dick Beyer
• [BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO   Dick Beyer
• [BioC] the error caused by makeProbePackage   Yingtao Bi
• [BioC] the error caused by makeProbePackage   Yingtao Bi
• [BioC] affymetrix chip type   Ben Bolstad
• [BioC] justRMA error message   Ben Bolstad
• [BioC] Sequence data and filtering   Justin Borevitz
• [BioC] venn diagram   Anthony Bosco
• [BioC] Problem with GOHyperG   Bosotti, Roberta [Nervianoms]
• [BioC] Problem with GOHyperG   Bosotti, Roberta [Nervianoms]
• [BioC] doing some math on an array of PM probes   Stuart Brown
• [BioC] vsn in limma or marray/arrayMagic   Andreas Buness
• [BioC] limma and normexp   Helen Cattan
• [BioC] reading Agilent data files   Giovanni Coppola
• [BioC] limma and p-values   Giovanni Coppola
• [BioC] limma and p-values   Giovanni Coppola
• [BioC] specifying a path in read.table on a Mac   John Cornell
• [BioC] Problem with specifying path in read.table on Mac solved   John Cornell
• [BioC] Re: [R] Configuration of memory usage   Peter Dalgaard
• [BioC] Clustering and gene modules   Sean Davis
• [BioC] Clustering and gene modules   Sean Davis
• [BioC] reading Agilent data files   Sean Davis
• [BioC] Significant p-values disappear in limma   Sean Davis
• [BioC] Significant p-values disappear in limma   Sean Davis
• [BioC] limma question   Sean Davis
• [BioC] GOstats   Sean Davis
• [BioC] (no subject)   Sean Davis
• [BioC] Yeast and LocuslinkIDs   Sean Davis
• [BioC] Yeast and LocuslinkIDs   Sean Davis
• [BioC] hgu133_plus_2?   Sean Davis
• [BioC] Problem with GOHyperG   Sean Davis
• [BioC] Problem with GOHyperG   Sean Davis
• [BioC] indexing geneNames in exprs   Sean Davis
• [BioC] Splitting a limma MAlist by a factor   Sean Davis
• [BioC] Custom CDF Files - howto ?   Rhonda DeCook
• [BioC] Custom CDF Files - howto ?   Rhonda DeCook
• [BioC] Import of high resolution .CEL files   Hrishikesh Deshmukh
• Re: [BioC] F-tests for factorial effects - limma   Ramon Diaz-Uriarte
• Re: [BioC] F-tests for factorial effects - limma   Ramon Diaz-Uriarte
• [BioC] dist{amap} error?   Radu Dobrin
• [BioC] GCRMA question   Radu Dobrin
• [BioC] Scaling GCRMA intesities   Radu Dobrin
• [BioC] affymetrix RNA degradation   Dr_Gyorffy_Balazs
• [BioC] Could anyone tell me how to check the code for image() function in Affy package?   Frank Duan
• [BioC] Could anyone tell me how to check the code for image() function in Affy package?   Frank Duan
• [BioC] webbioc upload manager error   Jose Duarte
• [BioC] graphs   Steffen Durinck
• [BioC] Mac binaries   Byron Ellis
• [BioC] installing meta packages on Unix   Seth Falcon
• [BioC] (no subject)   Seth Falcon
• [BioC] Bioconductor Install Problems   Seth Falcon
• [BioC] Upcoming changes to the Bioconductor website   Seth Falcon
• [BioC] Update on Bioconductor website changes   Seth Falcon
• [BioC] CDF/CEL binary conversion/support status ???   Richard Finney
• [BioC] Custom CDF Files - howto ?   Richard Finney
• [BioC] Custom CDF Files - howto ?   Richard Finney
• [BioC] Annotate package   Robert Gentleman
• [BioC] the error caused by makeProbePackage   Robert Gentleman
• [BioC] ontoTools and Rgraphviz   Robert Gentleman
• [BioC] Can't install tcl/tk on Mac OS 10.3.7   Robert Gentleman
• [BioC] annaffy's annotation update   Robert Gentleman
• [BioC] Installation memory demands (GO, humanLLMappings)   Robert Gentleman
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Robert Gentleman
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Robert Gentleman
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Robert Gentleman
• [BioC] Custom CDF Files - howto ?   Robert Gentleman
• [BioC] problem of package yg98 and XML   Robert Gentleman
• [BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO   Robert Gentleman
• [BioC] R --vanilla and Annotation pkg   Jeff Gentry
• [BioC] latest limma package   Jeff Gentry
• [BioC] GenomeViz   Ghai, Rohit
• [BioC] GenomeViz again : corrected link   Rohit Ghai
• [BioC] NCBI LocusLink -> Entrez Gene transition   Bubba Gump
• [BioC] limma question   Dianjing Guo
• [BioC] Re: Installing Bioconductor on R 1.9.1   Marion Hakanson
• [BioC] Installation memory demands (GO, humanLLMappings)   Marion Hakanson
• [BioC] mas5call select genes   Stephen Henderson
• [BioC] venn diagram   Laura Hollins
• [BioC] A question about Limma   Fangxin Hong
• [BioC] A question about Limma   Fangxin Hong
• [BioC] A question about Limma   Fangxin Hong
• [BioC] SAM vs. Limma   Fangxin Hong
• [BioC] A question about Limma   Fangxin Hong
• [BioC] Error message from running SAM for one-class case(siggenes)   Fangxin Hong
• BUGRe: [BioC] Error message from running SAM for one-class case(siggenes)   Fangxin Hong
• [BioC] problem with siggenes   Fangxin Hong
• [BioC] affy to normalize others single chanels...   Wolfgang Huber
• [BioC] Masamb-2005 conference announcement   Wolfgang Huber
• [BioC] the error caused by makeProbePackage   Wolfgang Huber
• [BioC] single-array error model   Wolfgang Huber
• [BioC] Job offer at EMBL Heidelberg   Wolfgang Huber
• [BioC] hgu95av2   Wolfgang Huber
• [BioC] order of PM from ReadAffy and probe$sequence   Wolfgang Huber
• [BioC] mas5call select genes   Wolfgang Huber
• [BioC] Re: Installing Bioconductor on R 1.9.1   Wolfgang Huber
• [BioC] Re: Installing Bioconductor on R 1.9.1   Wolfgang Huber
• [BioC] Re: Installing Bioconductor on R 1.9.1   Wolfgang Huber
• [BioC] MM > PM intensities   Wolfgang Huber
• [BioC] justRMA error message   Harry Hurd
• [BioC] mas5call select genes   Rafael Irizarry
• [BioC] affy to normalize others single chanels...   Rafael A. Irizarry
• [BioC] Soybean cdfenv   Ithal, Nagabhushana
• [BioC] Soybean CDFNV   Ithal, Nagabhushana
• [BioC] R --vanilla and Annotation pkg   Saurin Jani
• [BioC] R --vanilla and Annotation pkg   Saurin Jani
• [BioC] How can I extract Raw Intensities with Probe IDs on Affy Chips   Saurin Jani
• [BioC] How to get Raw Affy Chip Intensity after RMA   Saurin Jani
• [BioC] get GEO files and generate expression set HOW?   Saurin D. Jani
• [BioC] LIMMA makeContrasts(Groups[1]-Groups[2], levels = design) Error   Saurin D. Jani
• [BioC] GEO Files: queryGEO( ) question,   Saurin D. Jani
• [BioC] limma   Josephine
• [BioC] TAG3 script   Joshi, Nina (NIH/NCI)
• [BioC] ygs98   Christina Kendziorski
• [BioC] Example from help on GOHyperG   Christina Kendziorski
• [BioC] Yeast and LocuslinkIDs   Christina Kendziorski
• [BioC] Yeast and LocuslinkIDs   Christina Kendziorski
• [BioC] Mac binaries   Simon Kidd
• [BioC] Installation memory demands (GO, humanLLMappings)   Jan T. Kim
• [BioC] affy to normalize others single chanels...   Marcelo Luiz de Laia
• [BioC] Statistical design help before proceed with biological experiments   Marcelo Luiz de Laia
• [BioC] hu6800 annotation package amd mgu74cdf package   Josephine Liang
• [BioC] Dose-Response: Regressiion and ANOVA   Liaw, Andy
• [BioC] enquiry about errorest with model-knn   Liaw, Andy
• [BioC] leave-one-out cross validation for randomForest   Liu, Xin
• [BioC] enquiry about errorest with model-knn   Liu, Xin
• [BioC] Affymetrix CDF package   MShingyoji at lbl.gov
• [BioC] Soybean CDFNV   James MacDonald
• [BioC] Import of high resolution .CEL files   James MacDonald
• [BioC] Significant p-values disappear in limma   James W. MacDonald
• [BioC] doing some math on an array of PM probes   James W. MacDonald
• [BioC] affymetrix chip type   James W. MacDonald
• [BioC] hu6800 annotation package amd mgu74cdf package   James W. MacDonald
• [BioC] pamr / R graphics recording   James W. MacDonald
• [BioC] (no subject)   James W. MacDonald
• [BioC] affymetrix RNA degradation   James W. MacDonald
• [BioC] CDF/CEL binary conversion/support status ???   James W. MacDonald
• [BioC] hgu133_plus_2?   James W. MacDonald
• [BioC] Could anyone tell me how to check the code for image() function in Affy package?   James W. MacDonald
• [BioC] Logged or unlogged data for multtest and limma?   James W. MacDonald
• [BioC] Colours in degradation courve   James W. MacDonald
• [BioC] SAM False and FDR   Auer Michael
• [BioC] SAM vs. Limma   Auer Michael
• [BioC] cgh   Auer Michael
• [BioC] limma design matrix   Auer Michael
• [BioC] reading arrays image analysed with spot   Auer Michael
• [BioC] webbioc upload manager error   Jacob Michaelson
• [BioC] affy Yeast 2.0 annotation   Jacob Michaelson
• [BioC] Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf   Crispin Miller
• [BioC] Re: random location of duplicate spots and use of limma   Saroj Mohapatra
• [BioC] latest limma package   Nisha Mulakken
• [BioC] Testing two hypothesis by linear models   Ron Ophir
• [BioC] Tissue specific genes with limma   Ron Ophir
• [BioC] Error message when running arrayQuality 1.0.9   Paquet, Agnes
• [BioC] GOstats   Maria Persico
• [BioC] GOstats   Maria Persico
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Pita
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Pita
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Pita
• [BioC] Using limma with contrast matrix ,replicate spots,   Pita
• [BioC] latest limma package   Pita
• [BioC] multtest Paired T-test error   Katherine Pollard
• [BioC] mas5call select genes   Katleen De Preter
• [BioC] pamr / R graphics recording   Katleen De Preter
• [BioC] venn diagram   Katleen De Preter
• [BioC] search probe-ids for gene-symbols   Katleen De Preter
• [BioC] graphs   Katleen De Preter
• [BioC] GenBank Acc - Affy ProbeID   Katleen De Preter
• [BioC] reading arrays image analysed with spot   Tom Price
• [BioC] Error message when running arrayQuality 1.0.9   Longsi Ran
• [BioC] GenomeViz again : corrected link   A.J. Rossini
• [BioC] affymetrix chip type   Edoardo Saccenti
• [BioC] problem with siggenes   Edoardo Saccenti
• [BioC] after filtering   Edoardo Saccenti
• [BioC] managing GEO soft files   Edoardo Saccenti
• [BioC] gcrma   Lana Schaffer
• [BioC] gcrma   Lana Schaffer
• [BioC] installing meta packages on Unix   Lana Schaffer
• [BioC] order of PM from ReadAffy and probe$sequence   Lana Schaffer
• [BioC] hgu95av2   Lana Schaffer
• [BioC] MM > PM intensities   Lana Schaffer
• [BioC] indexing geneNames in exprs   Lana Schaffer
• [BioC] indexing geneNames in exprs   Lana Schaffer
• [BioC] enquiry about errorest with model-knn   Holger Schwender
• [BioC] problem with siggenes   Holger Schwender
• [BioC] limma design matrix   Shi, Tao
• [BioC] Problems building Bioconductor 1.5 on RHAW 3   Steve Simmons
• [BioC] Custom CDF files   Ken Simpson
• [BioC] random location of duplicate spots and use of limma   Jason Skelton
• [BioC] webbioc upload manager error   Colin Smith
• [BioC] Bioconductor Install Problems   Smith, Troy (NIH/NCI)
• [BioC] A question about Limma   Gordon Smyth
• [BioC] F-tests for factorial effects - limma   Gordon Smyth
• [BioC] limma design matrix   Gordon Smyth
• [BioC] Tissue specific genes with limma   Gordon Smyth
• [BioC] Two bioinformatics conferences in Sydney in July   Gordon Smyth
• [BioC] LIMMA:linear model and contrast.fit   Gordon Smyth
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Gordon Smyth
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Gordon Smyth
• [BioC] Splitting a limma MAlist by a factor   Gordon Smyth
• [BioC] A question about Limma   Gordon K Smyth
• [BioC] affy to normalize others single chanels...   Gordon K Smyth
• [BioC] limma and p-values   Gordon K Smyth
• [BioC] A question about Limma   Gordon K Smyth
• [BioC] limma and p-values   Gordon K Smyth
• [BioC] Fw: random location of duplicate spots and use of limma   Gordon K Smyth
• [BioC] limma and normexp   Gordon K Smyth
• [BioC] Limma, decideTests   Gordon K Smyth
• [BioC] vsn in limma or marray/arrayMagic   Gordon K Smyth
• [BioC] Using limma with contrast matrix ,replicate spots,   Gordon K Smyth
• [BioC] limma   Gordon K Smyth
• [BioC] Clustering and gene modules   Min-Han Tan
• [BioC] Clustering and gene modules   Min-Han Tan
• [BioC] pamr / R graphics recording   Min-Han Tan
• [BioC] problem of package yg98 and XML   Lin Tang
• [BioC] multtest Paired T-test error   Ken Termiso
• [BioC] Logged or unlogged data for multtest and limma?   Ken Termiso
• [BioC] single-array error model   Thibaud-Nissen, Francoise
• [BioC] LIMMA:linear model and contrast.fit   Sebastian Thieme
• [BioC] LIMMA:linear model and contrast.fit   Sebastian Thieme
• [BioC] Re: [R] Configuration of memory usage   R.G.W. Verhaak
• [BioC] hexbin 1.1-4 problem   Liviu M Vladutu
• [BioC] Can't install tcl/tk on Mac OS 10.3.7   Sam Volchenboum
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Chad Wayne
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Chad Wayne
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   Chad Wayne
• [BioC] Mac binaries   James Wettenhall
• [BioC] Mac binaries   James Wettenhall
• [BioC] Using limma with contrast matrix ,replicate spots, donor effects   Peter Wilkinson
• [BioC] mas5call select genes   Claire Wilson
• [BioC] SAM False and FDR   Wittner, Ben
• [BioC] gcrma   Zhijin Wu
• [BioC] gcrma   Zhijin Wu
• [BioC] gcrma / Bayes   Zhijin Wu
• [BioC] indexing geneNames in exprs   Zhijin Wu
• [BioC] Scaling GCRMA intesities   Zhijin Wu
• [BioC] gcrma 1.1.3 vs. gcrma 1.1.0   Zhijin Wu
• [BioC] gcRMA ....   Willy Wynant
• [BioC] gcrma / Bayes   Willy Wynant
• [BioC] gcrma / Bayes   Willy Wynant
• [BioC] Annotate package   Yihuan Xu
• [BioC] reading arrays image analysed with spot   Jean Yee Hwa Yang
• [BioC] (no subject)   Maria Ines Zanor
• [BioC] Annotate package   John Zhang
• [BioC] Problems installing KEGGSOAP   John Zhang
• [BioC] hu6800 Data package   John Zhang
• [BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO   John Zhang
• [BioC] html help links not updated after getBioC()   Yi-Xiong Zhou
• [BioC] ontoTools and Rgraphviz   Yi-Xiong Zhou
• [BioC] mark.pathway.by.objects return NULL   Yi-Xiong Zhou
• [BioC] Help on read.SMD() and read.SMD2()   Dongxiao Zhu
• [BioC] Affy Normalization--stable probeset option   alexpearlman at pearlquant.com
• [BioC] annaffy's annotation update   claudio.is at libero.it
• [BioC] Can't install tcl/tk on Mac OS 10.3.7   stefano iacus
• [BioC] Mac binaries   stefano iacus
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   stefano iacus
• [BioC] Affy 1.5.8 functions not working on Mac OS X 10.3   stefano iacus
• [BioC] Colours in degradation courve   kfbargad at lg.ehu.es
• [BioC] Imputations?   marcus
• [BioC] hgu133_plus_2?   marcus
• [BioC] IC 95% of kappa (intra-class coefficient)   myint.tin-tin-htar at jvr.ap-hop-paris.fr
• [BioC] gcrma 1.1.3 vs. gcrma 1.1.0   peter_lambert at agilent.com
• [BioC] Example from help on GOHyperG   jeffrey rasmussen
• [BioC] (no subject)   Jiuzhou song

Last message date: Mon Jan 31 21:30:08 CEST 2005
Archived on: Mon Jan 31 21:30:18 CEST 2005

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