October 2012 Archives by date

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Starting: Mon Oct 1 09:17:43 CEST 2012
Ending: Wed Oct 31 18:47:48 CET 2012
Messages: 633

• [BioC] DESeq plotting graphs.   PRAVIN
• [BioC] DESeq - working with more than 2 conditions   Natasha Sahgal
• [BioC] Possible to combine U133A&B Affy chip in one analysis?   Zaki Fadlullah
• [BioC] DESeq - working with more than 2 conditions   Vincenzo Capece
• [BioC] DESeq - working with more than 2 conditions   Thomas J Hardcastle
• [BioC] RNAseq object   René Böttcher [guest]
• [BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps   António Miguel de Jesus Domingues
• [BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps   Ou, Jianhong
• [BioC] Possible to combine U133A&B Affy chip in one analysis?   James W. MacDonald
• [BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps   António Miguel de Jesus Domingues
• [BioC] Fwd: DESeq plotting graphs.   Steve Lianoglou
• [BioC] RNAseq object   Tim Triche, Jr.
• [BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps   Ou, Jianhong
• [BioC] Error in makeTranscriptDbFromBiomart   Fabrice Tourre
• [BioC] shan   wang peter
• [BioC] sizepower   Michael Salbaum
• [BioC] ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps   Zhu, Lihua (Julie)
• [BioC] shan   Steve Lianoglou
• [BioC] shan   wang peter
• [BioC] Analyzing expression Affymetrix Hugene1.0.st array   Dario Strbenac
• [BioC] ANOVA in edgeR?   Gordon K Smyth
• [BioC] replace a value in a matrix using index   Mark B
• [BioC] RNAseq object   Nicolas Delhomme
• [BioC] warnings on easyRNASeq package   Nicolas Delhomme
• [BioC] ggplots2 - heatmap2 colour labels   Paolo Kunderfranco
• [BioC] replace a value in a matrix using index   Sean Davis
• [BioC] replace a value in a matrix using index   James W. MacDonald
• [BioC] normalizing two-color Agilent data from GEO...   Alan Derr
• [BioC] ggplots2 - heatmap2 colour labels   James W. MacDonald
• [BioC] enrichment + topGO   Maryam
• [BioC] ggplots2 - heatmap2 colour labels   Paolo Kunderfranco
• [BioC] enrichment + topGO   Paul Shannon
• [BioC] xps problem with root files   Juan Fernández Tajes
• [BioC] Granges averaging   Yannick Wurm
• [BioC] xps problem with root files   Benilton Carvalho
• [BioC] EdgeR condition-specific dispersion   Thomas Frederick Willems
• [BioC] shan   Steve Lianoglou
• [BioC] xps problem with root files   cstrato
• [BioC] xps problem with root files   cstrato
• [BioC] xps error   cstrato
• [BioC] cexRow problem   Alyaa Mahmoud
• [BioC] biomaRt error in scan file   Matthew McCormack
• [BioC] biomaRt error in scan file   Martin Morgan
• [BioC] biomaRt error in scan file   Dan Tenenbaum
• [BioC] biomaRt error in scan file   Matthew McCormack
• [BioC] PLGEM on metabolomic data?   Norman Pavelka
• [BioC] regarding the installation of packages   shivam agrawal [guest]
• [BioC] regarding the installation of packages   Dan Tenenbaum
• [BioC] regarding the installation of packages   Dan Tenenbaum
• [BioC] Regarding the commands for finding installed packages   manisha [guest]
• [BioC] Regarding the commands for finding installed packages   Christian Ruckert
• [BioC] Introns in exons and vice versa (Genomic Features)   Fenton Christopher Graham
• [BioC] Introns in exons and vice versa (Genomic Features)   Sean Davis
• [BioC] Introns in exons and vice versa (Genomic Features)   Alex Gutteridge
• [BioC] Introns in exons and vice versa (Genomic Features)   Fenton Christopher Graham
• [BioC] cexRow problem   James W. MacDonald
• [BioC] shan   wang peter
• [BioC] Error, while using produceGEOSampleInfoTemplate   Aliaksei Holik
• [BioC] readVcf - ALT allele as CompressedCharacterList instead of DNAStringSetList   Lescai, Francesco
• [BioC] irregular spacing exion miRNA microarry 7th generation   Christine Voellenkle [guest]
• [BioC] Assigning gene symbols to Affymetrix data and averaging probes   Hoyles, Lesley
• [BioC] Error, while using produceGEOSampleInfoTemplate   Tim Triche, Jr.
• [BioC] Assigning gene symbols to Affymetrix data and averaging probes   James W. MacDonald
• [BioC] regarding the installation of packages   Dan Tenenbaum
• [BioC] shan   Steve Lianoglou
• [BioC] readVcf - ALT allele as CompressedCharacterList instead of DNAStringSetList   Valerie Obenchain
• [BioC] Error in makeTranscriptDbFromBiomart   Cook, Malcolm
• [BioC] Assigning gene symbols to Affymetrix data and averaging probes   Hoyles, Lesley
• [BioC] Assigning gene symbols to Affymetrix data and averaging probes   James W. MacDonald
• [BioC] Granges averaging   Hervé Pagès
• [BioC] Granges averaging   Tengfei Yin
• [BioC] Bioconductor 2.11 is released   Dan Tenenbaum
• [BioC] Error in makeTranscriptDbFromBiomart   Martin Morgan
• [BioC] Error in makeTranscriptDbFromBiomart   Fabrice Tourre
• [BioC] Old Annotation Packages?   Hollis Wright
• [BioC] Error in makeTranscriptDbFromBiomart   Cook, Malcolm
• [BioC] Error in makeTranscriptDbFromBiomart   Dan Tenenbaum
• [BioC] warnings on easyRNASeq package   Mun Hua Tan
• [BioC] Error in makeTranscriptDbFromBiomart   Fabrice Tourre
• [BioC] Error while executing estimateCommonDisp   Surjyendu Ray [guest]
• [BioC] readVcf - ALT allele as CompressedCharacterList instead of DNAStringSetList   Lescai, Francesco
• [BioC] edgeR - no sequences are differentially expressed   Idit Buch
• [BioC] DEseq version and R version compatibility   José Luis Lavín
• [BioC] DEseq version and R version compatibility   José Luis Lavín
• [BioC] DEseq version and R version compatibility   Sean Davis
• [BioC] DEseq version and R version compatibility   Kasper Daniel Hansen
• [BioC] DEseq version and R version compatibility   José Luis Lavín
• [BioC] plotPCA error   Janake Wije [guest]
• [BioC] DEseq version and R version compatibility   Simon Anders
• [BioC] DEseq version and R version compatibility   Sean Davis
• [BioC] Old Annotation Packages?   James W. MacDonald
• [BioC] how to get normalized matrix   eyal avisar
• [BioC] DEseq version and R version compatibility   Steve Lianoglou
• [BioC] DEseq version and R version compatibility   Thomas Girke
• [BioC] DEseq version and R version compatibility   José Luis Lavín
• [BioC] DEseq version and R version compatibility   Nicolas Delhomme
• [BioC] DEseq version and R version compatibility   Steve Lianoglou
• [BioC] GGtools: transScores function returning cis eQTL   James Peters [guest]
• [BioC] GGtools: transScores function returning cis eQTL   Vincent Carey
• [BioC] LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric   Kripa R
• [BioC] LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric   James W. MacDonald
• [BioC] getBM weird error   Dick Beyer
• [BioC] DESeq - skewed MAplots and other problems   Michal Lulu
• [BioC] getBM weird error   James W. MacDonald
• [BioC] chromosome name match among vcf, txdb,BSgenome   sun
• [BioC] chromosome name match among vcf, txdb,BSgenome   Tim Triche, Jr.
• [BioC] GGtools: transScores function returning cis eQTL   Vincent Carey
• [BioC] GGtools: transScores function returning cis eQTL   Vincent Carey
• [BioC] getBM weird error   Dick Beyer
• [BioC] getBM weird error   James W. MacDonald
• [BioC] Query Error in biomaRt package on Mac R 2.15.1   Simon Senkewicz [guest]
• [BioC] Query Error in biomaRt package on Mac R 2.15.1   James W. MacDonald
• [BioC] chromosome name match among vcf, txdb,BSgenome   Hervé Pagès
• [BioC] edgeR - no sequences are differentially expressed   Mark Robinson
• [BioC] getBM weird error   Dick Beyer
• [BioC] how to get normalized matrix   Mark Robinson
• [BioC] getBM weird error   Dan Tenenbaum
• [BioC] EdgeR condition-specific dispersion   Mark Robinson
• [BioC] getBM weird error   Steffen Durinck
• [BioC] chromosome name match among vcf, txdb,BSgenome   Kasper Daniel Hansen
• [BioC] predictCoding() return empty Granges   sun
• [BioC] chromosome name match among vcf, txdb,BSgenome   Tim Triche, Jr.
• [BioC] getBM weird error   Dick Beyer
• [BioC] (no subject)   Michael
• [BioC] chromosome name match among vcf, txdb,BSgenome   Hervé Pagès
• [BioC] chromosome name match among vcf, txdb,BSgenome   Hervé Pagès
• [BioC] Error, while using produceGEOSampleInfoTemplate   Aliaksei Holik
• [BioC] Generating GEO submission files from beadarray summary data   Tim Triche, Jr.
• [BioC] predictCoding() return empty Granges   Valerie Obenchain
• [BioC] (no subject)   wang peter
• [BioC] Error while executing estimateCommonDisp   Gordon K Smyth
• [BioC] predictCoding() return empty Granges   Hervé Pagès
• [BioC] predictCoding() return empty Granges   Hervé Pagès
• [BioC] EdgeR condition-specific dispersion   Gordon K Smyth
• [BioC] Generating GEO submission files from beadarray summary data   Mark Dunning
• [BioC] Generating GEO submission files from beadarray summary data   Aliaksei Holik
• [BioC] DEseq version and R version compatibility   Wolfgang Huber
• [BioC] plotPCA error   Wolfgang Huber
• [BioC] GGtools: transScores function returning cis eQTL   Dr J. Peters
• [BioC] mixed-effects analysis within DEseq   Akiko Sugio
• [BioC] PCA plots and identifying outliers   Guest [guest]
• [BioC] PCA plots and identifying outliers   James W. MacDonald
• [BioC] PCA plots and identifying outliers   James W. MacDonald
• [BioC] PCA plots and identifying outliers   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] readVcf - ALT allele as CompressedCharacterList instead of DNAStringSetList   Valerie Obenchain
• [BioC] GEO newbie search question   Sylvain Foisy
• [BioC] PCA plots and identifying outliers   Tim Triche, Jr.
• [BioC] (no subject)   Michael
• [BioC] (no subject)   wang peter
• [BioC] predictCoding() return empty Granges   sun
• [BioC] (no subject)   Michael
• [BioC] predictCoding() return empty Granges   Hervé Pagès
• [BioC] predictCoding() return empty Granges   sun
• [BioC] predictCoding() return empty Granges   sun
• [BioC] GOSim Problem   Pablo Andretta Jaskowiak
• [BioC] issue with Views on PairwiseAlignmentsSingleSubject?   Janet Young
• [BioC] predictCoding() return empty Granges   Valerie Obenchain
• [BioC] issue with Views on PairwiseAlignmentsSingleSubject?   Hervé Pagès
• [BioC] Illumina SNP array annotation   Fabrice Tourre
• [BioC] DESeq diagnostics   Michael
• [BioC] DESeq diagnostics   Wolfgang Huber
• [BioC] DESeq diagnostics   Michael
• [BioC] goseq - data loading problem   Michael [guest]
• [BioC] coefs<-getAffinitySplineCoefficients...design error message help   Franklin Johnson [guest]
• [BioC] EBImage package now easier to install (no system dependencies)   Andrzej Oleś
• [BioC] goseq - data loading problem   Steve Lianoglou
• [BioC] EdgeR condition-specific dispersion   Robert Castelo
• [BioC] baySeq and samplesize factor   Fatemehsadat Seyednasrollah
• [BioC] Bioconductor Digest, Vol 116, Issue 8   Thomas J Hardcastle
• [BioC] NOISeq installation error   Fatemehsadat Seyednasrollah
• [BioC] NOISeq installation error   Sean Davis
• [BioC] NOISeq installation error   Fatemehsadat Seyednasrollah
• [BioC] NOISeq installation error   Sean Davis
• [BioC] coefs<-getAffinitySplineCoefficients...design error message help   Benilton Carvalho
• [BioC] NOISeq installation error   Martin Morgan
• [BioC] Illumina SNP array annotation   James W. MacDonald
• [BioC] Multiple Errors in the new cummerbund   Micheal [guest]
• [BioC] Multiple Errors in the new cummerbund   Michael
• [BioC] Multiple Errors in the new cummerbund   Michael
• [BioC] mixed-effects analysis within DEseq   Mike Love
• [BioC] Problem installing CummeRbund 2.0.0 (BiocGenerics)   Fluder, Eugene
• [BioC] Problem installing CummeRbund 2.0.0 (BiocGenerics)   Dan Tenenbaum
• [BioC] Fisher Information Matrix in edgeR   Ji, Tieming
• [BioC] DEXSeq offset term   Alicia Martin [guest]
• [BioC] gdata affects LumiBatch::combine method   Mark Cowley
• [BioC] Data filtering   Anand K.S.Rao [guest]
• [BioC] DEXSeq offset term   Alejandro Reyes
• [BioC] DESeq with 3 sample types   Sole Acha, Xavi
• [BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?   Ying Chen
• [BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?   Ying Chen
• [BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?   Marc Carlson
• [BioC] DEXSeq offset term   Alicia Martin
• [BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?   Ying Chen
• [BioC] How can I get the normalized read counts from TMM?   Reanne Bowlby
• [BioC] readVcf bgzip error   Davis, Brian
• [BioC] DEXSeq offset term   Simon Anders
• [BioC] gdata affects LumiBatch::combine method   Martin Morgan
• [BioC] DESeq diagnostics   Simon Anders
• [BioC] coefs<-getAffinitySplineCoefficients...design error message help   Benilton Carvalho
• [BioC] EBImage (>= 4.0.0) - browser-dependency display() issue   Robert Baer
• [BioC] readVcf bgzip error   Valerie Obenchain
• [BioC] EdgeR gof plot below line   Gordon K Smyth
• [BioC] can I use alignment utilities (mismatchTable, etc) on externally-generated alignments?   Janet Young
• [BioC] EdgeR for proteomics   Fabricio Marchini
• [BioC] DESeq diagnostics   Michael
• [BioC] Data filtering   Mark Robinson
• [BioC] NAs in snp.rhs.tests   maria traka (IFR)
• [BioC] New Bioconductor Package: SCAN.UPC   W. Evan Johnson
• [BioC] can I use alignment utilities (mismatchTable, etc) on externally-generated alignments?   Michael Lawrence
• [BioC] flowCore logicleTransform: handling NA values   Anja Mirenska
• [BioC] readVcf bgzip error   Davis, Brian
• [BioC] Data filtering   Steve Lianoglou
• [BioC] Profiles   Michael [guest]
• [BioC] Profiles   Steve Lianoglou
• [BioC] Profiles   Michael
• [BioC] Annotation databases--unable to get annotations   Manjula Kasoji [guest]
• [BioC] Error in .Call("R_shortRowNames", x, type, PACKAGE = "base") : "R_shortRowNames" not available for .Call() for package "base"   Tim Triche, Jr.
• [BioC] Annotation databases--unable to get annotations   James W. MacDonald
• [BioC] EdgeR for proteomics   Mark Robinson
• [BioC] EBImage (>= 4.0.0) - browser-dependency display() issue   Andrzej Oleś
• [BioC] bug in Biostrings mismatchTable?   Janet Young
• [BioC] Error in .Call("R_shortRowNames", x, type, PACKAGE = "base") : "R_shortRowNames" not available for .Call() for package "base"   Kasper Daniel Hansen
• [BioC] gdata affects LumiBatch::combine method   Mark Cowley
• [BioC] gdata affects LumiBatch::combine method   Martin Morgan
• [BioC] gdata affects LumiBatch::combine method   Mark Cowley
• [BioC] Error in .Call("R_shortRowNames", x, type, PACKAGE = "base") : "R_shortRowNames" not available for .Call() for package "base"   Hervé Pagès
• [BioC] gdata affects LumiBatch::combine method   Mark Cowley
• [BioC] How can I get the normalized read counts from TMM?   Mark Robinson
• [BioC] NOISeq initialization problem   sara wilson [guest]
• [BioC] odd results with pvclust   kh
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Fatemehsadat Seyednasrollah
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Marc Carlson
• [BioC] NOISeq initialization problem   Dan Tenenbaum
• [BioC] LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric   Kripa R
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Steve Lianoglou
• [BioC] LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric   James W. MacDonald
• [BioC] Limma; a kind of extended paired analyses with or without treatment   john herbert
• [BioC] Limma; a kind of extended paired analyses with or without treatment   James W. MacDonald
• [BioC] Limma; a kind of extended paired analyses with or without treatment   john herbert
• [BioC] Limma; a kind of extended paired analyses with or without treatment   James W. MacDonald
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Tim Triche, Jr.
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Steve Lianoglou
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Marc Carlson
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Michael Lawrence
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] interpretation & visualization methylation data (illum 450k)   Hooiveld, Guido
• [BioC] Question on survival   lau pel
• [BioC] Expression Values for SCAN.UPC?   Steve Piccolo
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Marc Carlson
• [BioC] interpretation & visualization methylation data (illum 450k)   Kasper Daniel Hansen
• [BioC] correcting for basal level of expression   Bogdan Tanasa
• [BioC] performance analytics- package   SheenMaria [guest]
• [BioC] performance analytics- package   SheenMaria [guest]
• [BioC] Limma; a kind of extended paired analyses with or without treatment   john herbert
• [BioC] get synthetic exon dataset with easyRNASeq   Nicolas Delhomme
• [BioC] bug in Biostrings mismatchTable?   Hervé Pagès
• [BioC] Help with Limma   Venu Pullabhatla
• [BioC] correcting for basal level of expression   Sean Davis
• [BioC] package grid   Khalid EL KARKOURI
• [BioC] odd results with pvclust   Stephen Turner
• [BioC] Mistake in the Limma documentation package read.maimages   Duarte Molha
• [BioC] Question on survival   James W. MacDonald
• [BioC] odd results with pvclust   Tim Triche, Jr.
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Marc Carlson
• [BioC] correcting for basal level of expression   Sean Davis
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Tim Triche, Jr.
• [BioC] readVcf bgzip error   Valerie Obenchain
• [BioC] readVcf bgzip error   Davis, Brian
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] Mistake in the Limma documentation package read.maimages   Gordon K Smyth
• [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?   Dana Most
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Fatemehsadat Seyednasrollah
• [BioC] BSgenome or org.Hs.eg.db to find gene length   Tim Triche, Jr.
• [BioC] package grid   Dan Tenenbaum
• [BioC] package grid   Kasper Daniel Hansen
• [BioC] package grid   Dan Tenenbaum
• [BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?   Benilton Carvalho
• [BioC] Limma; a kind of extended paired analyses with or without treatment   john herbert
• [BioC] Fisher Information Matrix in edgeR   Mark Robinson
• [BioC] limma topTable doesn't work without replicates [was: Help with limma]   Gordon K Smyth
• [BioC] package grid   Khalid EL KARKOURI
• [BioC] Multi-factor designs with specific comparisons   Tom [guest]
• [BioC] Need help: no MTC possible   suparna mitra
• [BioC] Post Doctoral Openings at University of Pittsburgh   Porterfield, Toni
• [BioC] edgeR: estimateGLMCommonDisp - Error in solve.default   Tom [guest]
• [BioC] question on easyRNASeq developer version   Nicolas Delhomme
• [BioC] trimTails function in ShortRead package give different results on the same input   Zhenyu Xu
• [BioC] Help with Limma   James W. MacDonald
• [BioC] edgeR: estimateGLMCommonDisp - Error in solve.default   James W. MacDonald
• [BioC] Need help: no MTC possible   James W. MacDonald
• [BioC] package grid   Dan Tenenbaum
• [BioC] Limma; a kind of extended paired analyses with or without treatment   James W. MacDonald
• [BioC] retrieve expression of all probes in the probe set   andrea.grilli at ior.it
• [BioC] package grid   Dan Tenenbaum
• [BioC] retrieve expression of all probes in the probe set   James W. MacDonald
• [BioC] EdgeR for proteomics   Fabricio Marchini
• [BioC] get al microRNA target sites for a given gene   Javier Pérez Florido
• [BioC] get al microRNA target sites for a given gene   James W. MacDonald
• [BioC] DESeq package   Maia de Oliveira, Julio
• [BioC] Rgraphviz: how to read a \"dot\" file?   Sam [guest]
• [BioC] package grid   Dan Tenenbaum
• [BioC] Rgraphviz: how to read a \"dot\" file?   Vincent Carey
• [BioC] limma topTable doesn't work without replicates [was: Help with limma]   Gordon K Smyth
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] Data filtering   Anand K S Rao
• [BioC] Rgraphviz: how to read a \"dot\" file?   Martin Morgan
• [BioC] Rsamtools Package Dereferences Symbolic Links   Lucas Swanson
• [BioC] Rgraphviz: how to read a \"dot\" file?   Kasper Daniel Hansen
• [BioC] Rgraphviz: how to read a \"dot\" file?   Sam Steingold
• [BioC] get al microRNA target sites for a given gene   Javier Pérez Florido
• [BioC] retrieve expression of all probes in the probe set   andrea.grilli at ior.it
• [BioC] Need help: no MTC possible   suparna mitra
• [BioC] NOISeq initialization problem   Sonia Tarazona
• [BioC] Need help: no MTC possible   suparna mitra
• [BioC] limma topTable doesn't work without replicates [was: Help with limma]   Venu Pullabhatla
• [BioC] Analysis of chIP-chip   John H [guest]
• [BioC] differentially expressed genes for multiple variables   priya [guest]
• [BioC] unable to install bioconductor package   mandar [guest]
• [BioC] differentially expressed genes for multiple variables   Steve Lianoglou
• [BioC] Need help: no MTC possible   James W. MacDonald
• [BioC] get al microRNA target sites for a given gene   James W. MacDonald
• [BioC] heatmap.2() get matrix after hierarchical clustering   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] heatmap.2() get matrix after hierarchical clustering   Guest [guest]
• [BioC] Rsamtools Package Dereferences Symbolic Links   Cook, Malcolm
• [BioC] Rsamtools Package Dereferences Symbolic Links   Vincent Carey
• [BioC] heatmap.2() get matrix after hierarchical clustering   James W. MacDonald
• [BioC] Rgraphviz: how to read a \"dot\" file?   Kasper Daniel Hansen
• [BioC] heatmap.2() get matrix after hierarchical clustering   Thomas Girke
• [BioC] heatmap.2() get matrix after hierarchical clustering   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Workshop on Statistical Genomics and Data Integration for Personalized Medicine   Darlene Goldstein
• [BioC] Need help: no MTC possible   suparna mitra
• [BioC] Need help: no MTC possible   James W. MacDonald
• [BioC] get al microRNA target sites for a given gene   James F. Reid
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] Rgraphviz: how to read a \"dot\" file?   Sam Steingold
• [BioC] package mcaGUI   Dan Tenenbaum
• [BioC] Rsamtools Package Dereferences Symbolic Links   Lucas Swanson
• [BioC] doesn\'t appear to be a valid BAM file   Michael [guest]
• [BioC] unable to install bioconductor package   Dan Tenenbaum
• [BioC] doesn\'t appear to be a valid BAM file   James W. MacDonald
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] GenomicRanges::nearest (especially follow)   Michael Lawrence
• [BioC] doesn\'t appear to be a valid BAM file   Steve Lianoglou
• [BioC] [igraph] Rgraphviz: how to read a \"dot\" file?   Gábor Csárdi
• [BioC] Rgraphviz: how to read a \"dot\" file?   Kasper Daniel Hansen
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] [igraph] Rgraphviz: how to read a \"dot\" file?   Gábor Csárdi
• [BioC] DESeq package   Bernd Fischer
• [BioC] GOstats different goDag size just changing the   Cristobal Fresno Rodríguez
• [BioC] GOstats different goDag size just changing the   James W. MacDonald
• [BioC] GenomicRanges::nearest (especially follow)   Hervé Pagès
• [BioC] Unable to download esets through GEOquery   T.Kartheeswaran [guest]
• [BioC] Unable to download esets through GEOquery   Sean Davis
• [BioC] ANOVA for gene ontology analysis   January Weiner
• [BioC] Analysis of chIP-chip   Joern Toedling
• [BioC] Reading in of Exon Array CEL files for normalization/ workflow   Jeremy Ng
• [BioC] Reading in of Exon Array CEL files for normalization/ workflow   Sean Davis
• [BioC] ChIPpeakAnno problem w getAllPeakSequence()   Anna Ehrlund
• [BioC] GOstats different goDag size just changing the   Cristobal Fresno Rodríguez
• [BioC] limma for finding differentialy expressed genes of several groups   priya [guest]
• [BioC] GOstats different goDag size just changing the   James W. MacDonald
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] limma for finding differentialy expressed genes of several groups   James W. MacDonald
• [BioC] limma for finding differentialy expressed genes of several groups   Sean Davis
• [BioC] GenomicRanges::nearest (especially follow)   Tim Triche, Jr.
• [BioC] [igraph] Rgraphviz: how to read a \"dot\" file?   Kasper Daniel Hansen
• [BioC] GenomicRanges::nearest (especially follow)   Cook, Malcolm
• [BioC] Rgraphviz plot with edge weights   Sam Steingold
• [BioC] ChIPpeakAnno problem w getAllPeakSequence()   Ou, Jianhong
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] ChIPpeakAnno problem w getAllPeakSequence()   Ou, Jianhong
• [BioC] Rsamtools Package Dereferences Symbolic Links   Martin Morgan
• [BioC] Rsamtools Package Dereferences Symbolic Links   Cook, Malcolm
• [BioC] GenomicRanges::nearest (especially follow)   Hervé Pagès
• [BioC] ChIPpeakAnno problem w getAllPeakSequence()   Anna Ehrlund
• [BioC] trimTails function in ShortRead package give different results on the same input   Martin Morgan
• [BioC] GeneNetworkBuilder package   Zhu, Lihua (Julie)
• [BioC] ANOVA for gene ontology analysis   Gordon K Smyth
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] limma for finding differentialy expressed genes of several groups   priya [guest]
• [BioC] limma for finding differentialy expressed genes of several groups   Sean Davis
• [BioC] limma for finding differentialy expressed genes of several groups   Sean Davis
• [BioC] filterBam using rname   rcaloger
• [BioC] Postdoc in Statistical Bioinformatics, Zurich, Switzerland   Mark Robinson
• [BioC] filterBam using rname   Valerie Obenchain
• [BioC] limma and legacy data   Simon Melov
• [BioC] Rsubread buildIndex: Too many sections in reference?   Wei Shi
• [BioC] rma and brightness of exon arrays   Rob Dunne
• [BioC] R matrix size limits and array data   Rob Dunne
• [BioC] LIMMA: question about design and contrasts   Patrick De Boever
• [BioC] EdgeR for proteomics   Mark Robinson
• [BioC] Data filtering   Mark Robinson
• [BioC] limma for finding differentialy expressed genes of several groups   Fabian Grammes
• [BioC] LIMMA: question about design and contrasts   James W. MacDonald
• [BioC] better security for bioconductor cloud ami   Ajay Ohri
• [BioC] Limma and multiple groups   Andrew Beggs [guest]
• [BioC] paired t test   Ingrid Mercier
• [BioC] Limma and multiple groups   James W. MacDonald
• [BioC] EdgeR GOF non-linear   Thomas Frederick Willems
• [BioC] Course Announcement - Next Generation Data Analysis with R/Bioc (Dec 6-10, 2012)   Thomas Girke
• [BioC] better security for bioconductor cloud ami   Dan Tenenbaum
• [BioC] 450K annotation: discrepancy between GEO GPL and Bioconductor annotation   Marc Carlson
• [BioC] New Bioconductor Package: SCAN.UPC   Steve Piccolo
• [BioC] New Bioconductor Package: SCAN.UPC   Steve Lianoglou
• [BioC] Help needed for limma analysis with a complex design.   He, Yiwen (NIH/CIT) [C]
• [BioC] regarding to flowCore/read.FCS warning message   Mike
• [BioC] flowCore/read.FCS issue   Mike
• [BioC] library(simpleaffy) error   Thornton, Matthew
• [BioC] makeProbePackage deprecated in AnnotationDbi ?   Hugh Shanahan
• [BioC] EdgeR GOF non-linear   Gordon K Smyth
• [BioC] Regarding CDF & annotation package   Gnanakkumaar P
• [BioC] R matrix size limits and array data   Benilton Carvalho
• [BioC] makeProbePackage deprecated in AnnotationDbi ?   Martin Morgan
• [BioC] poe.mcmc - metaArra non-numeric matrix extent error   Adrian Johnson
• [BioC] Help with installing genefilter -- "installed directory not writable"   Kee Pang SOH
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Dario Strbenac
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Steve Lianoglou
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Dario Strbenac
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Steve Lianoglou
• [BioC] Bimap Subsetting   Dario Strbenac
• [BioC] GenomicFeatures Transcripts Retrieval Fails   Dario Strbenac
• [BioC] Help with installing genefilter -- "installed directory not writable"   Dan Tenenbaum
• [BioC] Regarding CDF & annotation package   Hooiveld, Guido
• [BioC] annotation package building   Ingrid Mercier
• [BioC] R + SNOW scripts   Blesson Varghese
• [BioC] Creating annotation package with a new database schema   Fabian Grammes
• [BioC] poe.mcmc - metaArra non-numeric matrix extent error   Adrian Johnson
• [BioC] MetaArray - results - how to interpret   Adrian Johnson
• [BioC] Simpleaffy error : No methods found in "Biobase" for requests: geneNames   Thornton, Matthew
• [BioC] Bimap Subsetting   Hervé Pagès
• [BioC] MetaArray - results - how to interpret   Robert Scharpf
• [BioC] makeProbePackage deprecated in AnnotationDbi ?   Marc Carlson
• [BioC] Bimap Subsetting   Hervé Pagès
• [BioC] MetaArray - results - how to interpret   Adrian Johnson
• [BioC] Moving the ComBat user forum to the Bioconductor mailing list   W. Evan Johnson
• [BioC] Creating annotation package with a new database schema   Marc Carlson
• [BioC] rtracklayer 1.18 vignette bug in track()   J.T. Poirier
• [BioC] Creating annotation package with a new database schema   Hervé Pagès
• [BioC] R + SNOW scripts   Blesson Varghese
• [BioC] R + SNOW scripts   Dan Tenenbaum
• [BioC] R + SNOW scripts   Steve Lianoglou
• [BioC] R + SNOW scripts   Hervé Pagès
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] mouse4302.db and can't find gene symbol annotation   Andrew Yee
• [BioC] clustering in R   priya [guest]
• [BioC] experiment design in EdgeR   anna [guest]
• [BioC] help ith GeneAnswers / annotation package   Ingrid Mercier
• [BioC] EdgeR: paired samples together with independant samples   anna [guest]
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Hooiveld, Guido
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Tim Triche, Jr.
• [BioC] clustering in R   James W. MacDonald
• [BioC] mouse4302.db and can't find gene symbol annotation   James W. MacDonald
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Moiz Bootwalla
• [BioC] Sorting matrix by column   Guest [guest]
• [BioC] Sorting matrix by column   James W. MacDonald
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Sorting matrix by column   James W. MacDonald
• [BioC] Sorting matrix by column   James W. MacDonald
• [BioC] Sorting matrix by column   Axel Klenk
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Sorting matrix by column   James W. MacDonald
• [BioC] Sorting matrix by column   Axel Klenk
• [BioC] mouse4302.db and can't find gene symbol annotation   Andrew Yee
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Tim Triche, Jr.
• [BioC] annotation package building   Marc Carlson
• [BioC] mouse4302.db and can't find gene symbol annotation   Marc Carlson
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Sorting matrix by column   James W. MacDonald
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Hooiveld, Guido
• [BioC] problem with 'FDb.InfiniumMethylation.hg19'   Tim Triche, Jr.
• [BioC] Annotation using the affy package   Jens Lichtenberg [guest]
• [BioC] Creating annotation package with a new database schema   Fabian Grammes
• [BioC] any package can be used to do statistics of blast results   wang peter
• [BioC] better security for bioconductor cloud ami   Dan Tenenbaum
• [BioC] AnnotationDbi weirdness   James W. MacDonald
• [BioC] Annotation using the affy package   James W. MacDonald
• [BioC] Upgrading Bioconductor using BiocUpgrade   Lavinia Gordon
• [BioC] Upgrading Bioconductor using BiocUpgrade   Dan Tenenbaum
• [BioC] Upgrading Bioconductor using BiocUpgrade   Lavinia Gordon
• [BioC] experiment design in EdgeR   Gordon K Smyth
• [BioC] AnnotationDbi weirdness   Marc Carlson
• [BioC] How to get Gene ontology (GO) terms per probe   Rafi [guest]
• [BioC] AnnotationDbi weirdness   Marc Carlson
• [BioC] Why is writeVcf() slow?   hickey at wehi.EDU.AU
• [BioC] Fwd: covariate information   Cholhee Jung
• [BioC] Why is writeVcf() slow?   Valerie Obenchain
• [BioC] Why is writeVcf() slow?   Tim Triche, Jr.
• [BioC] Why is writeVcf() slow?   hickey at wehi.EDU.AU
• [BioC] Why is writeVcf() slow?   Michael Lawrence
• [BioC] inputting data in R   priya [guest]
• [BioC] Is it possible to reverse the normalized data ?   priya [guest]
• [BioC] EdgeR: how to save results for list of genes ?   anna [guest]
• [BioC] inputting data in R   Sean Davis
• [BioC] Is it possible to reverse the normalized data ?   Sean Davis
• [BioC] EdgeR: Problem with selection of highest transcript   anna [guest]
• [BioC] EdgeR: Problem with selection of highest transcript   Sean Davis
• [BioC] segfault during rma using oligo on Nimblegen data   Piet Jones
• [BioC] Annotation using the affy package   Jens Lichtenberg
• [BioC] Sorting matrix by column   Kasoji, Manjula (NIH/NCI) [C]
• [BioC] Annotation using the affy package   James W. MacDonald
• [BioC] GenomicRanges::nearest (especially follow)   Harris A. Jaffee
• [BioC] Fwd: covariate information   Achilleas Pitsillides
• [BioC] taqman versions   Marco Fabbri
• [BioC] EdgeR: paired samples together with independant samples   Gordon K Smyth
• [BioC] experiment design in EdgeR -- correction   Gordon K Smyth
• [BioC] EdgeR: how to save results for list of genes ?   Gordon K Smyth
• [BioC] taqman versions   James F. Reid
• [BioC] minimal number of features tested in edgeR   Stephanie [guest]
• [BioC] minimal number of features tested in edgeR   Mark Robinson
• [BioC] Fwd: covariate information   W. Evan Johnson
• [BioC] EdgeR: how to save results for list of genes ?   Nadira MRABET
• [BioC] EdgeR: how to save results for list of genes ?   Steve Lianoglou
• [BioC] Using edgeR with no replicates, estimating dispersion and the pseudo.alt slot   WATSON Mick
• [BioC] normalizing RNAseq with batch/block-level bulk DE   Aaron Mackey
• [BioC] segfault during rma using oligo on Nimblegen data   Benilton Carvalho
• [BioC] EdgeR: how to save results for list of genes ?   Nadira MRABET
• [BioC] How to get Gene ontology (GO) terms per probe   James W. MacDonald
• [BioC] recourse for errors with GEOquery::getGEO   Brent Pedersen
• [BioC] recourse for errors with GEOquery::getGEO   Sean Davis
• [BioC] GenomicRanges:::.filterMatchMatrix blows up nearest()   Harris A. Jaffee
• [BioC] GenomicRanges::nearest (especially follow)   Valerie Obenchain
• [BioC] normalizing RNAseq with batch/block-level bulk DE   Wolfgang Huber
• [BioC] normalizing RNAseq with batch/block-level bulk DE   Aaron Mackey
• [BioC] normalizing RNAseq with batch/block-level bulk DE   Wolfgang Huber
• [BioC] experiment design in EdgeR -- correction   anna [guest]
• [BioC] GenomicRanges:::.filterMatchMatrix blows up nearest()   Valerie Obenchain
• [BioC] Creating annotation package with a new database schema   Marc Carlson
• [BioC] Difference number of probesets after RMA with Oligo package and APT   Sophie Lamarre
• [BioC] Difference number of probesets after RMA with Oligo package and APT   Benilton Carvalho
• [BioC] Difference number of probesets after RMA with Oligo package and APT   Paul Geeleher
• [BioC] recourse for errors with GEOquery::getGEO   Sean Davis
• [BioC] covariate information   W. Evan Johnson
• [BioC] Using edgeR with no replicates, estimating dispersion and the pseudo.alt slot   Mark Robinson
• [BioC] EdgeR: Problem with selection of highest transcript   anna [guest]
• [BioC] [cellHTS2] error message with DualChannelScreen on example dataset   Vipin T Sreedharan
• [BioC] Opportunity - Informatics positions at Georetown University   Subha Madhavan
• [BioC] Why is writeVcf() slow?   Valerie Obenchain
• [BioC] Using edgeR with no replicates, estimating dispersion and the pseudo.alt slot   Gordon K Smyth
• [BioC] [cellHTS2] error message with DualChannelScreen on example dataset   Wolfgang Huber
• [BioC] codes for pairing   anna [guest]
• [BioC] rtracklayer 1.18 vignette bug in track()   Michael Lawrence
• [BioC] medain global normalize - argument matrix   Mark B
• [BioC] Convert Affy SNP array 0, 1, 2 to A C G T   Fabrice Tourre
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Holly
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Steve Lianoglou
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Steve Lianoglou
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Holly
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Holly
• [BioC] Convert Affy SNP array 0, 1, 2 to A C G T   Fabrice Tourre
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Holly
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Steve Lianoglou
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Steve Lianoglou
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Paul Shannon
• [BioC] EdgeR: dispersion and number of samples   anna [guest]
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Holly
• [BioC] How to get sequences corresponding to a GRanges?   Cei Abreu-Goodger
• [BioC] How to get sequences corresponding to a GRanges?   Martin Morgan
• [BioC] How to get sequences corresponding to a GRanges?   Cei Abreu-Goodger
• [BioC] Why is writeVcf() slow?   hickey at wehi.EDU.AU
• [BioC] GAGE: script   Aurelle [guest]
• [BioC] ComBat: Comparison of data   Peter Kupfer
• [BioC] ComBat: Comparison of data   Peter Kupfer
• [BioC] Extend GRanges start/end   António Miguel de Jesus Domingues
• [BioC] CHARM with Illumina 450K   Sole Acha, Xavi
• [BioC] segfault during rma using oligo on Nimblegen data   Piet Jones
• [BioC] Extend GRanges start/end   Paul Shannon
• [BioC] Extend GRanges start/end   Michael Lawrence
• [BioC] pam implementation   John Lande
• [BioC] segfault during rma using oligo on Nimblegen data   Benilton Carvalho
• [BioC] ComBat: Comparison of data   W. Evan Johnson
• [BioC] ComBat: Comparison of data   Peter Kupfer
• [BioC] ComBat: Comparison of data   W. Evan Johnson
• [BioC] Extend GRanges start/end   António Miguel de Jesus Domingues
• [BioC] A basic question about retrieve the absolute genome position from the output of of function matchPWM .   Paul Shannon
• [BioC] Extend GRanges start/end   António Miguel de Jesus Domingues
• [BioC] How to design matrix on edgeR to study genotype x environmental interaction   Daniela Lopes Paim Pinto
• [BioC] Extend GRanges start/end   António Miguel de Jesus Domingues
• [BioC] Extend GRanges start/end   Paul Shannon
• [BioC] Extend GRanges start/end   António Miguel de Jesus Domingues
• [BioC] CHARM with Illumina 450K   Tim Triche, Jr.
• [BioC] frma for Nimblegen arrays?   Hollis Wright
• [BioC] frma for Nimblegen arrays?   Matthew McCall
• [BioC] CHARM with Illumina 450K   Sole Acha, Xavi
• [BioC] frma for Nimblegen arrays?   Hollis Wright
• [BioC] Rle factors, table and empty levels   Peter Haverty
• [BioC] EdgeR: dispersion and number of samples   Gordon K Smyth
• [BioC] within chip probe replicates, Agilent chips   Reed, Tyler
• [BioC] Getting annotation into GOstat   Naomi Altman
• [BioC] Rle factors, table and empty levels   Valerie Obenchain
• [BioC] Problem installing goseq and RCurl   Dave Tang
• [BioC] RNA degradation plot of transcript arrays   Assa Yeroslaviz
• [BioC] frma for Nimblegen arrays?   Benilton Carvalho
• [BioC] how to write into a proper textfile from CEL files ?   priya [guest]
• [BioC] Problem installing goseq and RCurl   Dan Tenenbaum
• [BioC] how to write into a proper textfile from CEL files ?   WATSON Mick
• [BioC] Problem installing goseq and RCurl   Dave Tang
• [BioC] Problem installing goseq and RCurl   Dan Tenenbaum
• [BioC] how to write into a proper textfile from CEL files ?   WATSON Mick
• [BioC] RNA degradation plot of transcript arrays   James W. MacDonald
• [BioC] Getting annotation into GOstat   James W. MacDonald
• [BioC] pam implementation   John Lande
• [BioC] unbiased filtering of paired dataset   Hooiveld, Guido
• [BioC] frma for Nimblegen arrays?   Hollis Wright
• [BioC] a question about trimLRPatterns?   wang peter
• [BioC] Nimblegen microarray MM8_60mer_expr   Celine Mehats
• [BioC] frma for Nimblegen arrays?   Benilton Carvalho
• [BioC] KEGGgraph   Ricardo Silva
• [BioC] KEGGgraph   Paul Shannon
• [BioC] KEGGgraph   Ricardo Silva
• [BioC] a question about trimLRPatterns?   Hervé Pagès
• [BioC] a question about trimLRPatterns?   wang peter
• [BioC] KEGGgraph   Paul Shannon
• [BioC] KEGGgraph   Ricardo Silva
• [BioC] a question about trimLRPatterns?   Steve Lianoglou
• [BioC] a question about trimLRPatterns?   Steve Lianoglou
• [BioC] a question about trimLRPatterns?   Hervé Pagès
• [BioC] How to design matrix on edgeR to study genotype x environmental interaction   Gordon K Smyth
• [BioC] Problem installing goseq and RCurl   Dave Tang
• [BioC] Problem installing goseq and RCurl   Martin Morgan
• [BioC] bam files in sub-directories   René Böttcher [guest]
• [BioC] Passing multiple files to pdInfobuilder   Andrew Beggs [guest]
• [BioC] Passing multiple files to pdInfobuilder   Benilton Carvalho
• [BioC] Passing multiple files to pdInfobuilder   Andrew Beggs
• [BioC] Passing multiple files to pdInfobuilder   Benilton Carvalho
• [BioC] Passing multiple files to pdInfobuilder   Andrew Beggs
• [BioC] ComBat   SSc Array Core
• [BioC] EdgeR : CPM with names of genes   anna [guest]
• [BioC] HTqPCR with multiple samples in multiple cards   Ferran Briansó
• [BioC] bam files in sub-directories   Nicolas Delhomme
• [BioC] Basic questons about two-color array   Feng Tian

Last message date: Wed Oct 31 18:47:48 CET 2012
Archived on: Thu Nov 1 17:33:50 CET 2012

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