March 2010 Archives by author

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Starting: Mon Mar 1 02:56:27 CET 2010
Ending: Wed Mar 31 23:37:22 CEST 2010
Messages: 623

• [BioC] heatmap for high number of genes   michael watson (IAH-C)
• [BioC] chip-seq data analysis   michael watson (IAH-C)
• [BioC] where to download 'probeset.cvs' file for creating scheme file   michael watson (IAH-C)
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   michael watson (IAH-C)
• [BioC] log Fold Change   michael watson (IAH-C)
• [BioC] hclust for 13000 genes   michael watson (IAH-C)
• [BioC] hclust for 13000 genes   michael watson (IAH-C)
• [BioC] microRNA: which genes code for a specific mirna?   michael watson (IAH-C)
• [BioC] Get gene structure information: use biomaRt or other annotation packages?   michael watson (IAH-C)
• [BioC] Get gene structure information: use biomaRt or other annotation packages?   michael watson (IAH-C)
• [BioC] how to do cross species annotation?   michael watson (IAH-C)
• [BioC] R: error in gene2pathway results   Manca Marco (PATH)
• [BioC] IRanges RangedData - possible bug?   Patrick Aboyoun
• [BioC] BioC 2.6 New Package Submission Deadline - 3/31/10   Patrick Aboyoun
• [BioC] unable to load rtracklayer after install Iranges 1.5.56   Patrick Aboyoun
• [BioC] IRanges: setting score() on RangedData drops rownames   Patrick Aboyoun
• [BioC] IRanges: cbind not well defined for RangedData?   Patrick Aboyoun
• [BioC] IRanges: list columns in RangedData objects (was Re: IRanges: cbind not well defined for RangedData?)   Patrick Aboyoun
• [BioC] IRanges: list columns in RangedData objects (was Re: IRanges: cbind not well defined for RangedData?)   Patrick Aboyoun
• [BioC] IRanges: list columns in RangedData objects (was Re: IRanges: cbind not well defined for RangedData?)   Patrick Aboyoun
• [BioC] IRanges: as.matrix.RangesMatching not found with NAMESPACE   Patrick Aboyoun
• [BioC] Count differences between sequences   Patrick Aboyoun
• [BioC] Count differences between sequences   Patrick Aboyoun
• [BioC] Count differences between sequences   Patrick Aboyoun
• [BioC] GEOquery not working, NCBI changes?   Gad Abraham
• [BioC] GEOquery not working, NCBI changes?   Gad Abraham
• [BioC] GEOquery not working, NCBI changes?   Gad Abraham
• [BioC] microRNA: which genes code for a specific mirna?   Cei Abreu-Goodger
• [BioC] microRNA: which genes code for a specific mirna?   Cei Abreu-Goodger
• [BioC] microRNA: which genes code for a specific mirna?   Cei Abreu-Goodger
• [BioC] (no subject)   Naomi Altman
• [BioC] (no subject)   Naomi Altman
• [BioC] (no subject)   Naomi Altman
• [BioC] (no subject)   Naomi Altman
• [BioC] about formula in ancova   Naomi Altman
• [BioC] what is the website to get gene name from Affy probe set ID?   James Anderson
• [BioC] questions regarding simpleaffy and justMAS   James Anderson
• [BioC] question regarding qc function in simpleaffy package   James Anderson
• [BioC] spillover method in flowCore package   Frederico Arnoldi
• [BioC] spillover method in flowCore package   Frederico Arnoldi
• [BioC] Proxy issues   Jonathan Arthur
• [BioC] GDD or alternative   Jonathan Arthur
• [BioC] Kmeans help   sidahmed BENABDERRAHMANE
• [BioC] Kmeans help   Carlos J. Gil Bellosta
• [BioC] extract intensity values from .cel using Affy probe ids   Henrik Bengtsson
• [BioC] CN analysis on a small Affymetrix GWS6 data set (Was: Re: QC Affy 6.0 SNP arrays with crlmm or Oligo?)   Henrik Bengtsson
• [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6   Dick Beyer
• [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6   Dick Beyer
• [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6   Dick Beyer
• [BioC] Gene IDs returned by RankProd topGene command   Blumenberg, Miroslav
• [BioC] Zeros in ReadAffy was Re: farms package fails on estrogen data   Ben Bolstad
• [BioC] AffyPLM's MAplot and cex   Ben Bolstad
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Karl Brand
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Karl Brand
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Karl Brand
• [BioC] function similar to phyper function that can handle 3 or more gene lists   Karl Brand
• [BioC] [Bioc-sig-seq] ChIPpeakAnno get sequences from ranged data   Eric Bremer
• [BioC] clusterStab using a correlation distance   Daniel Brewer
• [BioC] Limma and logistic regression   Daniel Brewer
• [BioC] Limma and logistic regression   Daniel Brewer
• [BioC] GO's to gene's   Vincent Carey
• [BioC] multicore package and AnnotationDbi   Vincent Carey
• [BioC] getGEO - getting the .CEL files from GEO   Vincent Carey
• [BioC] GenomicFeatures question   Vincent Carey
• [BioC] GO's to gene's   Marc Carlson
• [BioC] A question about org.Hs.egMAPCOUNTS   Marc Carlson
• [BioC] Using annotation maps as environments in packages   Marc Carlson
• [BioC] what is the website to get gene name from Affy probe set ID?   Marc Carlson
• [BioC] org.Sc.sgd.db: ensembl id or entrez ID to GO term mapping   Marc Carlson
• [BioC] where is the "getHomolog" function in biomaRt?   Marc Carlson
• [BioC] building annotation package for porcine   Marc Carlson
• [BioC] GenomicFeatures question   Marc Carlson
• [BioC] "mogene10stv1cdf"   Marc Carlson
• [BioC] error in gene2pathway results   Marc Carlson
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] makePDpackage   Benilton Carvalho
• [BioC] makePDpackage   Benilton Carvalho
• [BioC] pd.mapping250k.XXX & genome build GRCh37/hg19   Benilton Carvalho
• [BioC] Problems with Downloading packages   Benilton Carvalho
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   Benilton Carvalho
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Benilton Carvalho
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   Benilton Carvalho
• [BioC] a question related to nested R loop   Benilton Carvalho
• [BioC] reverse engineering package   Robert Castelo
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   Tony Chiang
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   Tony Chiang
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   Tony Chiang
• [BioC] Clustering   Chintanu
• [BioC] Clustering   Chintanu
• [BioC] calculating heterozygosity, and genetic diversity   Coghlan, Avril
• [BioC] microRNA: which genes code for a specific mirna?   Kevin Coombes
• [BioC] checking multi-modalities in histograms   Kevin Coombes
• [BioC] checking multi-modalities in histograms   Kevin Coombes
• [BioC] gene2pathway: Error in pathIDsLev1   Jean-Pierre DESVIGNES
• [BioC] Heatmap: row labels & dendogram   Daniela
• [BioC] Heatmap: row labels & dendogram   Daniela
• [BioC] Heatmap: row labels & dendogram   Daniela
• [BioC] makePDpackage   Sean Davis
• [BioC] GO's to gene's   Sean Davis
• [BioC] GEOquery question -- suppressing download for GPL queries?   Sean Davis
• [BioC] mistmatch in GO terms between topGO_1.14.0 and org.Mm.eg.db_2.3.6   Sean Davis
• [BioC] GEOquery not working, NCBI changes?   Sean Davis
• [BioC] PCA or concordance   Sean Davis
• [BioC] hgu133a : probe ids to gene symbols   Sean Davis
• [BioC] chip-chip data   Sean Davis
• [BioC] chip-seq data analysis   Sean Davis
• [BioC] color key - heatmap.2   Sean Davis
• [BioC] AgiMicroRna package is not available at bioconductor or not in active form???   Sean Davis
• [BioC] Problems with Downloading packages   Sean Davis
• [BioC] AgiMicroRna package is not available at bioconductor or not in active form???   Sean Davis
• [BioC] problems when trying to use biomaRt   Sean Davis
• [BioC] AgiMicroRna package is not available at bioconductor or not in active form???   Sean Davis
• [BioC] Fwd: problems when trying to use biomaRt   Sean Davis
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Sean Davis
• [BioC] getGEO - getting the .CEL files from GEO   Sean Davis
• [BioC] hclust for 13000 genes   Sean Davis
• [BioC] microRNA: which genes code for a specific mirna?   Sean Davis
• [BioC] Tools for comparing microarray data on a snp level   Sean Davis
• [BioC] GEOquery problem   Sean Davis
• [BioC] Annotation for a GEO data set   Sean Davis
• [BioC] Using RCurl to upload CEL files to a LIMS   Sean Davis
• [BioC] Version package in release   Sean Davis
• [BioC] Agilent one colour   Sean Davis
• [BioC] Agilent one colour   Sean Davis
• [BioC] GCRMA Normalization Differences between Windows and MAC   Sean Davis
• [BioC] Error: cannot allocate vector of size 13.7 Mb   Sean Davis
• [BioC] Heatmap: row labels & dendogram   Sean Davis
• [BioC] Error: could not find function "mixedModel2Fit"   Sean Davis
• [BioC] Error: could not find function "mixedModel2Fit"   Sean Davis
• [BioC] simple functional analysis of gene lists   Sean Davis
• [BioC] Tools for comparing microarray data on a snp level   Vincent Davis
• [BioC] "mogene10stv1cdf"   Luqin Deng
• [BioC] GEOquery problem   Ding, Wei
• [BioC] Porting RWebServices from Axis1 to Axis2   Michael Dondrup
• [BioC] IRanges: setting score() on RangedData drops rownames   Michael Dondrup
• [BioC] IRanges: cbind not well defined for RangedData?   Michael Dondrup
• [BioC] IRanges: setting score() on RangedData drops rownames   Michael Dondrup
• [BioC] IRanges: cbind not well defined for RangedData?   Michael Dondrup
• [BioC] IRanges: as.matrix.RangesMatching not found with NAMESPACE   Michael Dondrup
• [BioC] IRanges: as.matrix.RangesMatching not found with NAMESPACE   Michael Dondrup
• [BioC] chip-chip data   Noah Dowell
• [BioC] chip-chip data   Noah Dowell
• [BioC] can't use weights in single channel analysis?   Jenny Drnevich
• [BioC] Limma-Contrasts-Question   Jenny Drnevich
• [BioC] problems when trying to use biomaRt   Jenny Drnevich
• [BioC] problems when trying to use biomaRt   Jenny Drnevich
• [BioC] problems when trying to use biomaRt   Jenny Drnevich
• [BioC] problems when trying to use biomaRt   Jenny Drnevich
• [BioC] Limma-Contrasts-Question   Jenny Drnevich
• [BioC] Heatmap: row labels & dendogram   Jenny Drnevich
• [BioC] removing probes from affybatch error   Jenny Drnevich
• [BioC] A statistical analyst or a post-doctoral position available immediately at Northwestern University   Pan Du
• [BioC] Call for papers: BCBGC-10, USA, July 2010   John Edward
• [BioC] Call for papers (Deadline Extended): BCBGC-10, USA, July 2010   John Edward
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] GO's to gene's   Loren Engrav
• [BioC] [MAANOVA] Warnings in fitmaanova & information request   Loren Engrav
• [BioC] [MAANOVA] Warnings in fitmaanova & information request   Loren Engrav
• [BioC] KEGGgraph fails on a KEGG XML file   Seth Falcon
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Seth Falcon
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Seth Falcon
• [BioC] farms package fails on estrogen data   Seth Falcon
• [BioC] MArray into data.frame for SPIA package   Seth Falcon
• [BioC] SPIA package   Seth Falcon
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Seth Falcon
• [BioC] Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package   Seth Falcon
• [BioC] Using RCurl to upload CEL files to a LIMS   Seth Falcon
• [BioC] Problem in running expresso command in affy package   Seth Falcon
• [BioC] Reg: normalization of ArrayExpress data   Rohit Farmer
• [BioC] Reg: normalization of ArrayExpress data   Rohit Farmer
• [BioC] Reg: normalization of ArrayExpress data   Rohit Farmer
• [BioC] Reg: T-statistic using limma   Rohit Farmer
• [BioC] Reg: T-statistic using limma   Rohit Farmer
• [BioC] Reg: T-statistic using limma   Rohit Farmer
• [BioC] problems when trying to use biomaRt   Juan Pablo Fededa
• [BioC] problems when trying to use biomaRt   Juan Pablo Fededa
• [BioC] problems when trying to use biomaRt   Juan Pablo Fededa
• [BioC] problems when trying to use biomaRt   Juan Pablo Fededa
• [BioC] problems when trying to use biomaRt   Juan Pablo Fededa
• [BioC] A question about org.Hs.egMAPCOUNTS   Gilbert Feng
• [BioC] error in limma read.images in linux ubuntu   Elmer Fernández
• [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems   Anthony Ferrari
• [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems   Anthony Ferrari
• [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems   Anthony Ferrari
• [BioC] KEGGgraph fails on a KEGG XML file   Chris Fjell
• [BioC] farms package fails on estrogen data   Javier Pérez Florido
• [BioC] building annotation package for porcine   Javier Pérez Florido
• [BioC] checking multi-modalities in histograms   Javier Pérez Florido
• [BioC] checking multi-modalities in histograms   Javier Pérez Florido
• [BioC] checking multi-modalities in histograms   Javier Pérez Florido
• [BioC] Accessing median and IQR values of MAplots   Javier Pérez Florido
• [BioC] limma lmFit error: Coefficients not estimable   Freydin, Maxim
• [BioC] limma lmFit error: Coefficients not estimable   Freydin, Maxim
• [BioC] limma lmFit error: Coefficients not estimable   Freydin, Maxim
• [BioC] Ecoli antisense library   Balasubramanian Ganesan
• [BioC] Ecoli antisense library   Balasubramanian Ganesan
• [BioC] Ecoli antisense library   Balasubramanian Ganesan
• [BioC] retrieveGenomicFeatureAnnotation.R file supplied with Ringo   Paul Geeleher
• [BioC] retrieveGenomicFeatureAnnotation.R file supplied with Ringo   Paul Geeleher
• [BioC] P-values to Z-scores   Paul Geeleher
• [BioC] KEGGgraph: retrieveKGML error (due to wrong ftp path)   Ludwig Geistlinger
• [BioC] Time-course microarray tutorial   Colin Gillespie
• [BioC] Protein Codes to Protein Names   Giulio Di Giovanni
• [BioC] read.DNAStringSet   Thomas Girke
• [BioC] intersection between genes and pathways   Alberto Goldoni
• [BioC] help on reading Agilent 44k 2 colour   Alberto Goldoni
• [BioC] help on reading Agilent 44k 2 colour   Alberto Goldoni
• [BioC] error in gene2pathway results   Alberto Goldoni
• [BioC] error in gene2pathway results   Alberto Goldoni
• [BioC] spillover method in flowCore package   Nishant Gopalakrishnan
• [BioC] silent data corruption in flowFlowJo, and fix   Gosink, John
• [BioC] Annotation for a GEO data set   Joern Grame
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Ivan Gregoretti
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Ivan Gregoretti
• [BioC] Fwd: regarding installaion of cdf package   Groot, Philip de
• [BioC] KEGGgraph fails on a KEGG XML file   Rajarshi Guha
• [BioC] KEGGgraph fails on a KEGG XML file   Rajarshi Guha
• [BioC] rawQ Affymetrix   Dr Balazs Gyorffy
• [BioC] PCA or concordance   Johnny H
• [BioC] PCA or concordance   Johnny H
• [BioC] about formula in ancova   RICHARD M. HEIBERGER
• [BioC] about formula in ancova   RICHARD M. HEIBERGER
• [BioC] [R] about the possible errors in Rgraphviz Package   HU,ZHENGJUN
• [BioC] [R] about the possible errors in Rgraphviz Package   HU,ZHENGJUN
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Florian Hahne
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Florian Hahne
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Kasper Daniel Hansen
• [BioC] 64-bit R - problem with affxparser   Kasper Daniel Hansen
• [BioC] GCRMA Normalization Differences between Windows and MAC   Kasper Daniel Hansen
• [BioC] 64-bit R - problem with affxparser   Kasper Daniel Hansen
• [BioC] Limma: technical replicates in multi-group design   Kasper Daniel Hansen
• [BioC] Help on Cosmo back ground model   Prashantha Hebbar
• [BioC] R package for analyzing MS/MS spectra   Prashantha Hebbar
• [BioC] Cosmo background model   Prashantha Hebbar
• [BioC] Cosmo Background model   Prashantha Hebbar
• [BioC] Cosmo Background model   Prashantha Hebbar
• [BioC] Package for Agilent microdata   Hersh
• [BioC] experience with rankproduct vs. limma - combining results   Hildebrand, Georg
• [BioC] Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package   John Holden
• [BioC] Using annotation maps as environments in packages   Antti Honkela
• [BioC] Using annotation maps as environments in packages   Antti Honkela
• [BioC] Using annotation maps as environments in packages   Antti Honkela
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   Hotz, Hans-Rudolf
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   Hotz, Hans-Rudolf
• [BioC] Reg: normalization of ArrayExpress data   Wolfgang Huber
• [BioC] Filter over group averages   Wolfgang Huber
• [BioC] Computational Biology Positions at EMBL (Heidelberg)   Wolfgang Huber
• [BioC] annotation in Ensembl using biomart   Wolfgang Huber
• [BioC] annotation in Ensembl using biomart   Wolfgang Huber
• [BioC] R/Maanova Tutorial   Wolfgang Huber
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   Wolfgang Huber
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   Wolfgang Huber
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Wolfgang Huber
• [BioC] Package for Agilent microdata   Wolfgang Huber
• [BioC] package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes   Wolfgang Huber
• [BioC] BiomaRt query   Wolfgang Huber
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Wolfgang Huber
• [BioC] where is the "getHomolog" function in biomaRt?   Wolfgang Huber
• [BioC] biomaRt - ensembl - proxy - NCBI36/hg18 - problems   Wolfgang Huber
• [BioC] GCRMA Normalization Differences between Windows and MAC   Wolfgang Huber
• [BioC] checking multi-modalities in histograms   Wolfgang Huber
• [BioC] Heatmap: row labels & dendogram   Melanie Huntley
• [BioC] Filter over group averages   Michael Imbeault
• [BioC] what is the website to get gene name from Affy probe set ID?   Michael Imbeault
• [BioC] 64-bit R - problem with affxparser   Michael Imbeault
• [BioC] 64-bit R - problem with affxparser   Michael Imbeault
• [BioC] 64-bit R - problem with affxparser   Michael Imbeault
• [BioC] color key - heatmap.2   Amit Indap
• [BioC] Xlaevis probe sequence file for gcRMA not found.   Naoki Irie
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Ivanek, Robert
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Ivanek, Robert
• [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow   Ivanek, Robert
• [BioC] affycomp updated in release branch   Harris A. Jaffee
• [BioC] Problem in running affy package   Priyanka Jain
• [BioC] Problem in running expresso command in affy package   Priyanka Jain
• [BioC] SNP plotter package   Kay Jaja
• [BioC] log Fold Change   Jay
• [BioC] pd.mapping250k.XXX & genome build GRCh37/hg19   Geoff Jentry
• [BioC] pd.mapping250k.XXX & genome build GRCh37/hg19   Geoff Jentry
• [BioC] Using RCurl to upload CEL files to a LIMS   Geoff Jentry
• [BioC] 64-bit R   Jin, Jp
• [BioC] Limma-Contrasts-Question   Biju Joseph
• [BioC] Limma-Contrasts-Question   Biju Joseph
• [BioC] Limma-Contrasts-Question   Biju Joseph
• [BioC] Loop design - biological, technical replication and contrasts   Maciej Jończyk
• [BioC] Loop design - biological, technical replication and contrasts   Maciej Jończyk
• [BioC] Loop design - biological, technical replication and contrasts   Maciej Jończyk
• [BioC] Loop design - biological, technical replication   Maciej Jończyk
• [BioC] [MAANOVA] Warnings in fitmaanova & information request   Maciej Jończyk
• [BioC] [MAANOVA] Warnings in fitmaanova & information request   Maciej Jończyk
• [BioC] Error in getCdfInfo(object)   Arun A K
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Audrey Kauffmann
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Audrey Kauffmann
• [BioC] Limma: technical replicates in multi-group design   Adam Kiezun
• [BioC] Limma: technical replicates in multi-group design   Adam Kiezun
• [BioC] Limma: technical replicates in multi-group design   Adam Kiezun
• [BioC] Ensembl mart release 57: Useful information   Rhoda Kinsella
• [BioC] how to do cross species annotation?   Alexandre Kuhn
• [BioC] Problems installing Bioconductor Affy on Windows 7   Marissa LaMadrid
• [BioC] affyPara: background correction & normalization only?   Leo Lahti
• [BioC] affyPara: background correction & normalization only?   Leo Lahti
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Michael Lawrence
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Michael Lawrence
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Michael Lawrence
• [BioC] rtrackalyer too slow?   Michael Lawrence
• [BioC] IRanges: cbind not well defined for RangedData?   Michael Lawrence
• [BioC] IRanges: list columns in RangedData objects (was Re: IRanges: cbind not well defined for RangedData?)   Michael Lawrence
• [BioC] IRanges: list columns in RangedData objects (was Re: IRanges: cbind not well defined for RangedData?)   Michael Lawrence
• [BioC] GDD or alternative   Michael Lawrence
• [BioC] Count differences between sequences   Michael Lawrence
• [BioC] fast iterator over DNAString's?   Paul Leo
• [BioC] GenomicFeatures question   Paul Leo
• [BioC] silent data corruption in flowFlowJo, and fix   Hin-Tak Leung
• [BioC] chip-seq data analysis   Tiandao Li
• [BioC] help on reading Agilent 44k 2 colour   Yong Li
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Steve Lianoglou
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Steve Lianoglou
• [BioC] heatmap for high number of genes   Steve Lianoglou
• [BioC] heatmap for high number of genes   Steve Lianoglou
• [BioC] PCA or concordance   Steve Lianoglou
• [BioC] ensembl annotation coordinate did not match that from UCSC genome browser using ucscTableQuery   Steve Lianoglou
• [BioC] fast iterator over DNAString's?   Steve Lianoglou
• [BioC] hclust for 13000 genes   Steve Lianoglou
• [BioC] hclust for 13000 genes   Steve Lianoglou
• [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?   Benoit Loup
• [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?   Benoit Loup
• [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?   Benoit Loup
• [BioC] annotation in Ensembl using biomart   Jason Lu
• [BioC] annotation in Ensembl using biomart   Jason Lu
• [BioC] filtering in GSEABase package   Jason Lu
• [BioC] Ecoli antisense library   James MacDonald
• [BioC] Error in getCdfInfo(object)   James MacDonald
• [BioC] removing probes from affybatch error   James MacDonald
• [BioC] stuck with affy/ limma   James MacDonald
• [BioC] Search queries with biomaRt does not align with online queries via ensembl   James W. MacDonald
• [BioC] Xlaevis probe sequence file for gcRMA not found.   James W. MacDonald
• [BioC] clusterStab using a correlation distance   James W. MacDonald
• [BioC] (no subject)   James W. MacDonald
• [BioC] Ecoli antisense library   James W. MacDonald
• [BioC] Ecoli antisense library   James W. MacDonald
• [BioC] questions regarding simpleaffy and justMAS   James W. MacDonald
• [BioC] Ecoli antisense library   James W. MacDonald
• [BioC] Error: could not find function "mixedModel2Fit"   James W. MacDonald
• [BioC] How to create a design matrix for a three-way design?   James W. MacDonald
• [BioC] Limma: technical replicates in multi-group design   James W. MacDonald
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Koen Marien
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Koen Marien
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Koen Marien
• [BioC] stuck with affy/limma   Maxim
• [BioC] stuck with affy/ limma   Maxim
• [BioC] Limma and logistic regression   Claus Mayer
• [BioC] Reg: T-statistic using limma   Claus Mayer
• [BioC] Reg: T-statistic using limma   Claus Mayer
• [BioC] Heatmap: row labels & dendogram   Saroj K Mohapatra
• [BioC] Heatmap: row labels & dendogram   Saroj K Mohapatra
• [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?   Saroj K Mohapatra
• [BioC] GO's to gene's   Martin Morgan
• [BioC] GO's to gene's   Martin Morgan
• [BioC] Porting RWebServices from Axis1 to Axis2   Martin Morgan
• [BioC] GO's to gene's   Martin Morgan
• [BioC] GO's to gene's   Martin Morgan
• [BioC] GO's to gene's   Martin Morgan
• [BioC] where to download 'probeset.cvs' file for creating scheme file   Martin Morgan
• [BioC] Problems installing Bioconductor Affy on Windows 7   Martin Morgan
• [BioC] Problems with Downloading packages   Martin Morgan
• [BioC] farms package fails on estrogen data   Martin Morgan
• [BioC] problems when trying to use biomaRt   Martin Morgan
• [BioC] problems when trying to use biomaRt   Martin Morgan
• [BioC] problems when trying to use biomaRt   Martin Morgan
• [BioC] Zeros in ReadAffy was Re: farms package fails on estrogen data   Martin Morgan
• [BioC] GO.db and org.XX.eg.db: update frequency?   Martin Morgan
• [BioC] Question about iFlow   Martin Morgan
• [BioC] Version package in release   Martin Morgan
• [BioC] 64-bit R   Martin Morgan
• [BioC] Version package in release   Martin Morgan
• [BioC] 64-bit R - problem with affxparser   Martin Morgan
• [BioC] Count differences between sequences   Martin Morgan
• [BioC] error in limma read.images in linux ubuntu   Martin Morgan
• [BioC] Count differences between sequences   Martin Morgan
• [BioC] Count differences between sequences   Martin Morgan
• [BioC] Count differences between sequences   Martin Morgan
• [BioC] COURSE: Microarray Analysis in R (Bioconductor) from Imperial College   North, Bernard V
• [BioC] simple functional analysis of gene lists   Juan Carlos Oliveros
• [BioC] read.DNAStringSet   Ron Ophir
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Mikhail Pachkov
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Mikhail Pachkov
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Mikhail Pachkov
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Mikhail Pachkov
• [BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene   Mikhail Pachkov
• [BioC] Mapping using absolute coordinates   Ludo Pagie
• [BioC] A question about org.Hs.egMAPCOUNTS   Hervé Pagès
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   Hervé Pagès
• [BioC] getSeq error with multiple inqueries, BSgenome   Hervé Pagès
• [BioC] Using annotation maps as environments in packages   Hervé Pagès
• [BioC] trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem   Hervé Pagès
• [BioC] A question about org.Hs.egMAPCOUNTS   Hervé Pagès
• [BioC] question about forgeBSgenomeDataPkg function   Hervé Pagès
• [BioC] fast iterator over DNAString's?   Hervé Pagès
• [BioC] fast iterator over DNAString's?   Hervé Pagès
• [BioC] Count differences between sequences   Hervé Pagès
• [BioC] Count differences between sequences   Hervé Pagès
• [BioC] Count differences between sequences   Hervé Pagès
• [BioC] Count differences between sequences   Hervé Pagès
• [BioC] Count differences between sequences   Hervé Pagès
• [BioC] BiomaRt query   De Boever Patrick
• [BioC] P-values to Z-scores   Francois Pepin
• [BioC] Version package in release   Pierre-Yves
• [BioC] Version package in release   Pierre-Yves
• [BioC] Version package in release   Pierre-Yves
• [BioC] Version package in release   Pierre-Yves
• [BioC] SPIA package   Marcos Pinho
• [BioC] MArray into data.frame for SPIA package   Marcos Pinho
• [BioC] hclust for 13000 genes   David K Pritchard
• [BioC] Problems with Downloading packages   Abbhirami Rajagopal
• [BioC] Problems with Downloading packages   Abbhirami Rajagopal
• [BioC] Question about iFlow   Abbhirami Rajagopal
• [BioC] Question about plateCore   Abbhirami Rajagopal
• [BioC] getGEO - getting the .CEL files from GEO   Tim Rayner
• [BioC] filtering in GSEABase package   James F. Reid
• [BioC] microRNA: which genes code for a specific mirna?   Robinson, Peter
• [BioC] Protein Codes to Protein Names   Cristobal Fresno Rodríguez
• [BioC] KEGGgraph: retrieveKGML error (due to wrong ftp path)   Cristobal Fresno Rodríguez
• [BioC] readMicroRnaAFE function in AgiMicroR package   Pedro López Romero
• [BioC] extract intensity values from .cel using Affy probe ids   Rinku Saha
• [BioC] Not loading flowViz package   Sancho, Jose
• [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth   Deepayan Sarkar
• [BioC] affyPara: background correction & normalization only?   Markus Schmidberger
• [BioC] affyPara: background correction & normalization only?   Markus Schmidberger
• [BioC] affyPara: background correction & normalization only?   Markus Schmidberger
• [BioC] fast iterator over DNAString's?   Paul Shannon
• [BioC] Problem with xps package installation on Mac platform   Steve Shen
• [BioC] Problem with xps package installation on Mac platform   Steve Shen
• [BioC] where to download 'probeset.cvs' file for creating scheme file   Steve Shen
• [BioC] where to download 'probeset.cvs' file for creating scheme file   Steve Shen
• [BioC] where to download 'probeset.cvs' file for creating scheme file   Steve Shen
• [BioC] xps import data derived from different batches   Steve Shen
• [BioC] xps import data derived from different batches   Steve Shen
• [BioC] xps import data derived from different batches   Steve Shen
• [BioC] xps import data derived from different batches   Steve Shen
• [BioC] xps import data derived from different batches   Steve Shen
• [BioC] xps: returns only 21 records   Steve Shen
• [BioC] xps: convert a data frame to ExprTreeSet   Steve Shen
• [BioC] xps: returns only 21 records   Steve Shen
• [BioC] (no subject)   Pete Shepard
• [BioC] Limma: technical replicates in multi-group design   Wei Shi
• [BioC] reverse engineering package   Weiwei Shi
• [BioC] Rintact equivalent in BioC2.6?   Fraser Sim
• [BioC] Svar: Bioconductor Digest, Vol 85, Issue 28   Vibe Henriette Skov
• [BioC] Beadarray data manipulation   Mike Smith
• [BioC] hgu133a : probe ids to gene symbols   Tim Smith
• [BioC] microRNA: which genes code for a specific mirna?   Tim Smith
• [BioC] microRNA: which genes code for a specific mirna?   Tim Smith
• [BioC] microRNA: which genes code for a specific mirna?   Tim Smith
• [BioC] Loop design - biological, technical replication and contrasts   Gordon K Smyth
• [BioC] Loop design - biological, technical replication   Gordon K Smyth
• [BioC] can't use weights in single channel analysis?   Gordon K Smyth
• [BioC] Limma-Contrasts-Question   Gordon K Smyth
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   Gordon K Smyth
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   Gordon K Smyth
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   Gordon K Smyth
• [BioC] MArray into data.frame for SPIA package   Gordon K Smyth
• [BioC] Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package   Gordon K Smyth
• [BioC] limma lmFit error: Coefficients not estimable   Gordon K Smyth
• [BioC] limma lmFit error: Coefficients not estimable   Gordon K Smyth
• [BioC] error in limma read.images in linux ubuntu   Gordon K Smyth
• [BioC] Limma: technical replicates in multi-group design   Gordon K Smyth
• [BioC] (no subject)   Ana Staninska
• [BioC] limma: duplicate spots, technical replicates and biological replicates   Ana Staninska
• [BioC] (no subject)   Ana Staninska
• [BioC] (no subject)   Ana Staninska
• [BioC] about formula in ancova   Juan Pedro Steibel
• [BioC] R/Maanova Tutorial   Juan Pedro Steibel
• [BioC] intersection between genes and pathways   John Stevens
• [BioC] Question about plateCore   Errol Strain
• [BioC] Agilent one colour   Yogi Sundaravadanam
• [BioC] Agilent one colour   Yogi Sundaravadanam
• [BioC] Beadarray data manipulation   Ramzi TEMANNI
• [BioC] Job: Bioinformatics Data Analyst in Vienna, Austria   Ido M. Tamir
• [BioC] R package for analyzing MS/MS spectra   Kishor Tappita
• [BioC] affymetrix gene level arrays - cdf issue   Stefanie Tauber
• [BioC] simple functional analysis of gene lists   Rainer Tischler
• [BioC] retrieveGenomicFeatureAnnotation.R file supplied with Ringo   Joern Toedling
• [BioC] chip-chip data   Joern Toedling
• [BioC] chip-chip data   Joern Toedling
• [BioC] chip-chip data   Joern Toedling
• [BioC] Tools for comparing microarray data on a snp level   Tim Triche
• [BioC] R/Maanova Tutorial   Ricardo Verdugo
• [BioC] R/Maanova Tutorial   Ricardo Verdugo
• [BioC] Limma: technical replicates in multi-group design   Mike Walter
• [BioC] How to create a design matrix for a three-way design?   January Weiner
• [BioC] Averaging duplicate probes in an RGList object   Tom Wenseleers
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan.   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] Issue with limma and normalization of Agilent data generated with a 20-bit scan   White, Peter
• [BioC] microRNA: which genes code for a specific mirna?   Chao-Jen Wong
• [BioC] Question about iFlow   Chao-Jen Wong
• [BioC] Not loading flowViz package   Chao-Jen Wong
• [BioC] Problem in running affy package   Chao-Jen Wong
• [BioC] Count differences between sequences   Erik Wright
• [BioC] Count differences between sequences   Erik Wright
• [BioC] AffyPLM's MAplot and cex   Timothy Wu
• [BioC] rtrackalyer too slow?   Wu, Xiwei
• [BioC] GCRMA Normalization Differences between Windows and MAC   Zhijin Wu
• [BioC] trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem   Andrew Yee
• [BioC] trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem   Andrew Yee
• [BioC] trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem   Andrew Yee
• [BioC] IRanges RangedData - possible bug?   Janet Young
• [BioC] request: calculate coverage with weight on RangedData object   Janet Young
• [BioC] LIMMA Array Weight analysis   GAO Yu
• [BioC] KEGGgraph fails on a KEGG XML file   Jitao David Zhang
• [BioC] Rintact equivalent in BioC2.6?   Jitao David Zhang
• [BioC] about formula in ancova   Dejian Zhao
• [BioC] about formula in ancova   Dejian Zhao
• [BioC] about formula in ancova   Dejian Zhao
• [BioC] about formula in ancova   Dejian Zhao
• [BioC] R/Maanova Tutorial   Dejian Zhao
• [BioC] R/Maanova Tutorial   Dejian Zhao
• [BioC] R / R+ Webminar *** R-PLUS Rocks: Interactive, Comprehensible and Highly Visual. March 12th @ 12PM ET (USA Time)   Zheng, Xin (NIH) [C]
• [BioC] a new bridge between bioperl and bioconductor   Zheng, Xin (NIH) [C]
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function   Zhu, Julie
• [BioC] Favor: ChIPpeakAnno   Zhu, Julie
• [BioC] GO.db and org.XX.eg.db: update frequency?   Zhu, Julie
• [BioC] GO.db and org.XX.eg.db: update frequency?   Zhu, Julie
• [BioC] Get gene structure information: use biomaRt or other annotation packages?   Zhu, Julie
• [BioC] Get gene structure information: use biomaRt or other annotation packages?   Zhu, Julie
• [BioC] ChIPpeakAnno get sequences from ranged data   Zhu, Julie
• [BioC] org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem   Zhu, Julie
• [BioC] org.Sc.sgd.db: ensembl id or entrez ID to GO term mapping   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno get sequences from ranged data   Zhu, Julie
• [BioC] [Bioc-sig-seq] ChIPpeakAnno get sequences from ranged data   Zhu, Julie
• [BioC] Help on Cosmo   Prashantha Hebbar Kiradi [MU-MLSC]
• [BioC] Loop design - biological, technical replication and contrasts   avehna
• [BioC] heatmap for high number of genes   avehna
• [BioC] heatmap for high number of genes   avehna
• [BioC] heatmap for high number of genes   avehna
• [BioC] heatmap for high number of genes   avehna
• [BioC] hclust for 13000 genes   avehna
• [BioC] hclust for 13000 genes   avehna
• [BioC] hclust for 13000 genes   avehna
• [BioC] makePDpackage   somnath bandyopadhyay
• [BioC] makePDpackage   somnath bandyopadhyay
• [BioC] chip-chip data   somnath bandyopadhyay
• [BioC] chip-chip data   somnath bandyopadhyay
• [BioC] chip-chip data   somnath bandyopadhyay
• [BioC] Spillover method in flowCore   Perry_D_Haaland at bd.com
• [BioC] farms package fails on estrogen data   bmb at bmbolstad.com
• [BioC] Count differences between sequences   erikwright at comcast.net
• [BioC] Count differences between sequences   erikwright at comcast.net
• [BioC] FW: Bioconductor   Dana.Stanley at csiro.au
• [BioC] Problem with xps package installation on Mac platform   cstrato
• [BioC] Problem with xps package installation on Mac platform   cstrato
• [BioC] where to download 'probeset.cvs' file for creating scheme file   cstrato
• [BioC] where to download 'probeset.cvs' file for creating scheme file   cstrato
• [BioC] where to download 'probeset.cvs' file for creating scheme file   cstrato
• [BioC] xps import data derived from different batches   cstrato
• [BioC] xps import data derived from different batches   cstrato
• [BioC] xps: returns only 21 records   cstrato
• [BioC] xps: convert a data frame to ExprTreeSet   cstrato
• [BioC] Heatmap: row labels & dendogram   danieladna
• [BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?   J.delasHeras at ed.ac.uk
• [BioC] pair information of microRNA and Targets prediction   jrwang at itri.org.tw
• [BioC] a question related to nested R loop   aiguo li
• [BioC] GCRMA Normalization Differences between Windows and MAC   martin martinez
• [BioC] Using RCurl to upload CEL files to a LIMS   stephen at mnemosyne.co.uk
• [BioC] Using RCurl to upload CEL files to a LIMS   stephen at mnemosyne.co.uk
• [BioC] Using RCurl to upload CEL files to a LIMS   stephen at mnemosyne.co.uk
• [BioC] Using RCurl to upload CEL files to a LIMS   stephen at mnemosyne.co.uk
• [BioC] multicore package and AnnotationDbi   stephen.rudd at orionpharma.com
• [BioC] regarding making of probe package   sneha patil
• [BioC] Fwd: regarding making of probe package   sneha patil
• [BioC] regarding installaion of cdf package   sneha patil
• [BioC] Fwd: regarding installaion of cdf package   sneha patil
• [BioC] AgiMicroRna package is not available at bioconductor or not in active form???   neeraj rana
• [BioC] Error: cannot allocate vector of size 13.7 Mb   neeraj rana
• [BioC] Error: could not find function "mixedModel2Fit"   neeraj rana
• [BioC] landscape genetics analysis   milton ruser
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] getSeq error with multiple inqueries, BSgenome   sabrina s
• [BioC] how to use rtracklayer to retrieve sequence of list of coordinates   sabrina s
• [BioC] getSeq error with multiple inqueries, BSgenome   sabrina s
• [BioC] ensembl annotation coordinate did not match that from UCSC genome browser using ucscTableQuery   sabrina s
• [BioC] ensembl annotation coordinate did not match that from UCSC genome browser using ucscTableQuery   sabrina s
• [BioC] unable to load rtracklayer after install Iranges 1.5.56   sabrina s
• [BioC] unable to load rtracklayer after install Iranges 1.5.56   sabrina s
• [BioC] Problem with xps package installation on Mac platform   steve shen
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   jeremy wilson
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   jeremy wilson
• [BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?   jeremy wilson
• [BioC] readMicroRnaAFE function in AgiMicroR package   heyi xiao
• [BioC] R / R+ Webminar *** R-PLUS Rocks: Interactive, Comprehensible and Highly Visual. March 12th @ 12PM ET (USA Time)   sue at xlsolutions-corp.com
• [BioC] March-April 2010*** R / S+ Essentials and Advanced Courses*** by XLSolutions Corp in San Francisco and other USA cities   sue at xlsolutions-corp.com
• [BioC] how to do cross species annotation?   zrl
• [BioC] how to do cross species annotation?   zrl
• [BioC] how to do cross species annotation?   zrl
• [BioC] where is the "getHomolog" function in biomaRt?   zrl
• [BioC] where is the "getHomolog" function in biomaRt?   zrl
• [BioC] getGEO - getting the .CEL files from GEO   張 語恬

Last message date: Wed Mar 31 23:37:22 CEST 2010
Archived on: Thu Apr 1 18:23:21 CEST 2010

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