March 2014 Archives by thread

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Starting: Sat Mar 1 00:44:24 CET 2014
Ending: Mon Mar 31 23:43:18 CEST 2014
Messages: 552

• [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hooiveld, Guido
  • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hervé Pagès
    • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hooiveld, Guido
      • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Michael Stadler
      • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hooiveld, Guido
      • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hans-Rudolf Hotz
      • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hervé Pagès
      • [BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5   Hooiveld, Guido
• [BioC] parsing discrete colors in pathview KEGG   Luo Weijun
• [BioC] CIGAR-aware coverage   Hervé Pagès
• [BioC] question regarding function IMA.methy450PP in IMA package   Jack Luo
• [BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection   Sindre Lee
  • [BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection   Ryan
    • [BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection   Ryan
  • [BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection   Yunshun Chen
• [BioC] CSAMA 2014: Computational Statistics for Genome Biology - June 22-27, 2014   Wolfgang Huber
• [BioC] Questiond about the descrepancy between edgeR and limma-voom   Yunshun Chen
  • [BioC] Questiond about the descrepancy between edgeR and limma-voom   Ming Yi
  • [BioC] Questiond about the descrepancy between edgeR and limma-voom   Ming Yi
    • [BioC] Questiond about the descrepancy between edgeR and limma-voom   Yunshun Chen
• [BioC] Annotation different expressed exon. results from DESeq   Fabrice Tourre
  • [BioC] Annotation different expressed exon. results from DESeq   Alejandro Reyes
    • [BioC] Annotation different expressed exon. results from DESeq   Jose Garcia
      • [BioC] Annotation different expressed exon. results from DESeq   Alejandro Reyes
    • [BioC] Annotation different expressed exon. results from DESeq   Fabrice Tourre
• [BioC] Low number of replicates DESeq   Federico Gaiti
  • [BioC] Low number of replicates DESeq   Michael Love
    • [BioC] Low number of replicates DESeq   Federico Gaiti
    • [BioC] Low number of replicates DESeq   Federico Gaiti
      • [BioC] Low number of replicates DESeq   Michael Love
      • [BioC] Low number of replicates DESeq   Steve Lianoglou
      • [BioC] Low number of replicates DESeq   Federico Gaiti
      • [BioC] Low number of replicates DESeq   Steve Lianoglou
• [BioC] Old packages for new version of r   Ahmed Arslan [guest]
  • [BioC] Old packages for new version of r   James W. MacDonald
• [BioC] DMR identification: minfi speed, memory problems   Allegra A. Petti
• [BioC] Problems with robustPca in pcaMethods   Julian Gehring
  • [BioC] Problems with robustPca in pcaMethods   Henrik Bengtsson
    • [BioC] Problems with robustPca in pcaMethods   Henning Redestig
    • [BioC] Problems with robustPca in pcaMethods   Julian Gehring
• [BioC] Gviz: axes related parameters   Hahne, Florian
• [BioC] DiffBind and paired end data   Rory Stark
  • [BioC] DiffBind and paired end data   Rory Stark
    • [BioC] DiffBind and paired end data   Federico Marini
      • [BioC] DiffBind and paired end data   Rory Stark
      • [BioC] DiffBind and paired end data   Federico Marini
      • [BioC] DiffBind and paired end data   Federico Marini
      • [BioC] DiffBind and paired end data   Rory Stark
      • [BioC] DiffBind and paired end data   Federico Marini
      • [BioC] DiffBind and paired end data   Federico Marini
• [BioC] results interpretation   Leonardo Pitombo [guest]
  • [BioC] results interpretation   Michael Love
• [BioC] Error message with DESeqDataSet   Yoong [guest]
  • [BioC] Error message with DESeqDataSet   Michael Love
    • [BioC] Error message with DESeqDataSet   FeiYian Yoong
      • [BioC] Error message with DESeqDataSet   Michael Love
      • [BioC] Error message with DESeqDataSet   FeiYian Yoong
      • [BioC] Error message with DESeqDataSet   Michael Love
      • [BioC] Error message with DESeqDataSet   Michael Love
      • [BioC] Error message with DESeqDataSet   FeiYian Yoong
• [BioC] DART   Lawler, Katherine
• [BioC] limma contrast matrix interaction effect   steven wink
  • [BioC] limma contrast matrix interaction effect   Dario Strbenac
  • [BioC] limma contrast matrix interaction effect   Gordon K Smyth
    • [BioC] limma contrast matrix interaction effect   steven wink
      • [BioC] limma contrast matrix interaction effect   Gordon K Smyth
      • [BioC] limma contrast matrix interaction effect   steven wink
• [BioC] DESeq2 in R_devel: a bug?   Sylvain Foisy Ph. D.
  • [BioC] DESeq2 in R_devel: a bug?   Michael Love
    • [BioC] DESeq2 in R_devel: a bug?   Sylvain Foisy Ph. D.
      • [BioC] DESeq2 in R_devel: a bug?   Michael Love
      • [BioC] DESeq2 in R_devel: a bug?   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Michael Love
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Sean Davis
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
      • [BioC] Questions about multi-factor contrast setting in DESeq2   Ming Yi
• [BioC] Help with DMPFinder in minfi package   smeeta
• [BioC] Rosetta Resolver-like error-weighted ANOVAs in Bioconductor   Ida Hatoum
  • [BioC] Rosetta Resolver-like error-weighted ANOVAs in Bioconductor   Ryan C. Thompson
• [BioC] BigWig Import by Chromosome   Dario Strbenac
  • [BioC] BigWig Import by Chromosome   Martin Morgan
• [BioC] Select different linear models in voom   Francesco [guest]
  • [BioC] Select different linear models in voom   Gordon K Smyth
    • [BioC] Select different linear models in voom   Francesco Gatto
      • [BioC] Select different linear models in voom   Gordon K Smyth
• [BioC] code not shown in the manual, page 31.   Son Pham
• [BioC] code not shown in EdgeR manual.   Son Pham
  • [BioC] code not shown in EdgeR manual.   James W. MacDonald
• [BioC] Fwd: Re: request for help in minfi-dmpFinder   Smeeta shrestha
• [BioC] model.matrix   Mike Miller
  • [BioC] model.matrix   Gordon K Smyth
• [BioC] DESeq2 comparison of treatment in two conditions   Kauer Max
  • [BioC] DESeq2 comparison of treatment in two conditions   Michael Love
• [BioC] SPIA   Martin [guest]
  • [BioC] SPIA   Tarca, Adi
• [BioC] edgeR, design matrix not of full rank   Georg Otto
• [BioC] Version 1.3.4   Yoong [guest]
  • [BioC] Version 1.3.4   Michael Love
• [BioC] aggregate genes in DEXSeq   xiayu
  • [BioC] aggregate genes in DEXSeq   Alejandro Reyes
• [BioC] sum the values with same ID   guest [guest]
  • [BioC] sum the values with same ID   Hervé Pagès
• [BioC] VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?   Thornton, Matthew
  • [BioC] VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?   Wolfgang Huber
• [BioC] Can we apply WGCNA to RNA-seq dataset?   spano spano
  • [BioC] Can we apply WGCNA to RNA-seq dataset?   Peter Langfelder
• [BioC] CummeRbund getGenes command broken in R?   Zain Alvi [guest]
  • [BioC] CummeRbund getGenes command broken in R?   Loyal A. Goff
    • [BioC] CummeRbund getGenes command broken in R?   Zain A Alvi
• [BioC] Limma : Single Channel experiment design matrix   Koran [guest]
  • [BioC] Limma : Single Channel experiment design matrix   James W. MacDonald
• [BioC] svg error in arrayQualityMetrics   Straubhaar, Juerg
  • [BioC] svg error in arrayQualityMetrics   Wolfgang Huber
    • [BioC] svg error in arrayQualityMetrics   Straubhaar, Juerg
      • [BioC] svg error in arrayQualityMetrics   Wolfgang Huber
  • [BioC] svg error in arrayQualityMetrics   Andrzej Oleś
• [BioC] About ChIPpeakAnno   Lucia Peixoto
  • [BioC] About ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] About ChIPpeakAnno   Lucia Peixoto
    • [BioC] About ChIPpeakAnno   Zhu, Lihua (Julie)
      • [BioC] About ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] Extracting strand information from GenomicFeatures transcript db objects   Veerendra Gadekar
  • [BioC] Extracting strand information from GenomicFeatures transcript db objects   Hervé Pagès
    • [BioC] Extracting strand information from GenomicFeatures transcript db objects   Hervé Pagès
      • [BioC] Extracting strand information from GenomicFeatures transcript db objects   Hervé Pagès
      • [BioC] Extracting strand information from GenomicFeatures transcript db objects   Veerendra Gadekar
• [BioC] maSigPro RNAseq data (counts=TRUE will not work for negative binomial)   Audra Andrew [guest]
  • [BioC] maSigPro RNAseq data (counts=TRUE will not work for negativebinomial)   Mª José Nueda
• [BioC] edgeR time series analysis question   Audra Andrew [guest]
  • [BioC] edgeR time series analysis question   Gordon K Smyth
• [BioC] maSigPro counts=TRUE negative binomial trouble   Audra Andrew [guest]
• [BioC] Help with sliding window analysis on GRanges object   Stefano Iantorno
  • [BioC] Help with sliding window analysis on GRanges object   Martin Morgan
  • [BioC] Help with sliding window analysis on GRanges object   Michael Lawrence
    • [BioC] Help with sliding window analysis on GRanges object   Michael Lawrence
      • [BioC] Help with sliding window analysis on GRanges object   Stefano Iantorno
• [BioC] error on heatmap   guest [guest]
  • [BioC] error on heatmap   Joseph Nathaniel Paulson
• [BioC] Filter out genes with small profile variance from gene expression data   Jerry Cholo
  • [BioC] Filter out genes with small profile variance from gene expression data   Martin Morgan
    • [BioC] Input regarding sorting out candidate genes from edgeR results   Sindre Lee
      • [BioC] Input regarding sorting out candidate genes from edgeR results   Steve Lianoglou
• [BioC] Quick question about Chromosome names using Tophat2 and Cufflinks w/Ensembl NCBIM37   Sindre Lee
  • [BioC] Quick question about Chromosome names using Tophat2 and Cufflinks w/Ensembl NCBIM37   James W. MacDonald
• [BioC] dexseq zero length exons   Jose Garcia
  • [BioC] dexseq zero length exons   Alejandro Reyes
    • [BioC] dexseq zero length exons   Jose Garcia
• [BioC] B score-like posterior log-odds for edgeR topTags?   Aaron Mackey
• [BioC] IRanges::Rle::[ arguably should return NA when i is out of range   Cook, Malcolm
  • [BioC] IRanges::Rle::[ arguably should return NA when i is out of range   Hervé Pagès
    • [BioC] IRanges::Rle::[ arguably should return NA when i is out of range   Michael Lawrence
• [BioC] mouseData in heatmap of metagenomeSeq package   guest [guest]
  • [BioC] mouseData in heatmap of metagenomeSeq package   Joseph Nathaniel Paulson
• [BioC] using other ontologies in topGO && building GO.db like database for GO-like ontologies   Xin.H
• [BioC] Conference Announcement - CAMDA 2014   Djork-Arné Clevert
• [BioC] multiple groups time course RNA Seq LIMMA   Riba Michela
  • [BioC] multiple groups time course RNA Seq LIMMA   Gordon K Smyth
    • [BioC] multiple groups time course RNA Seq LIMMA   Riba Michela
      • [BioC] multiple groups time course RNA Seq LIMMA   Gordon K Smyth
• [BioC] ChIPpeakAnno   Bahar
• [BioC] DESeq2 error: inv(): matrix appears to be singular   Hugo Varet
  • [BioC] DESeq2 error: inv(): matrix appears to be singular   Michael Love
    • [BioC] DESeq2 error: inv(): matrix appears to be singular   Hugo Varet
      • [BioC] DESeq2 error: inv(): matrix appears to be singular   Michael Love
      • [BioC] DESeq2 error: inv(): matrix appears to be singular   Michael Love
      • [BioC] DESeq2 error: inv(): matrix appears to be singular   Michael Love
      • [BioC] DESeq2 error: inv(): matrix appears to be singular   Hugo Varet
• [BioC] question on MotifDb package   Paul Shannon
• [BioC] Finding genes with similar trend   Christian De Santis
  • [BioC] Finding genes with similar trend   Steve Lianoglou
    • [BioC] Finding genes with similar trend   Christian De Santis
• [BioC] edgeR design matrix, one group vs average of other groups   Georg Otto
  • [BioC] How to draw cbioportal's oncoprint plot in R?   ying chen
  • [BioC] edgeR design matrix, one group vs average of other groups   Yunshun Chen
    • [BioC] edgeR design matrix, one group vs average of other groups   Ming Yi
  • [BioC] edgeR design matrix, one group vs average of other groups   Ryan
  • [BioC] edgeR design matrix, one group vs average of other groups   Yunshun Chen
  • [BioC] edgeR design matrix, one group vs average of other groups   Georg Otto
  • [BioC] edgeR design matrix, one group vs average of other groups   Gordon K Smyth
• [BioC] Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?   Nick Fishbane
• [BioC] EdgeR classic vs. glm   Son Pham
  • [BioC] EdgeR classic vs. glm   Yunshun Chen
    • [BioC] EdgeR classic vs. glm   Son Pham
      • [BioC] EdgeR classic vs. glm   Ryan C. Thompson
• [BioC] problem in making cdf package_makecdfenv   amit kumar subudhi
  • [BioC] problem in making cdf package_makecdfenv   James W. MacDonald
• [BioC] Repitools - featureScores - mappability Bsgenome object   Dario Strbenac
• [BioC] GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories   Dale Richardson
• [BioC] GOseq at a specific level ?   amandine.fournier at chu-lyon.fr
  • [BioC] GOseq at a specific level ?   Nadia Davidson
• [BioC] Can I input ordinal variables into a model in Limma?   Scott Robinson
  • [BioC] Can I input ordinal variables into a model in Limma?   Gordon K Smyth
• [BioC] biomaRt and rma   Naomi Altman
  • [BioC] biomaRt and rma   Naomi Altman
  • [BioC] biomaRt and rma   James W. MacDonald
• [BioC] Contrasts result interpretation   Yoong [guest]
  • [BioC] Contrasts result interpretation   Michael Love
• [BioC] error of makeTranscriptDbFromGFF   DL Guo [guest]
  • [BioC] [devteam-bioc] error of makeTranscriptDbFromGFF   Marc Carlson
• [BioC] GAGE/Pathview RNA-Seq Workflows: reference genome issue   Luo Weijun
• [BioC] fatal error when installint BioC devel on R devel   Martin Rijlaarsdam
  • [BioC] fatal error when installint BioC devel on R devel   Martin Rijlaarsdam
• [BioC] Statistical Bioinformatician/Geneticist in Oxford   Stephen Taylor
  • [BioC] DEXSeq output - count file   Rao,Xiayu
    • [BioC] DEXSeq output - count file   Alejandro Reyes
    • [BioC] DEXSeq output - count file   Jose Garcia
    • [BioC] DEXSeq output - count file   Jose Garcia
    • [BioC] DEXSeq output - count file   Alejandro Reyes
• [BioC] LIMMA/VOOM: Using and Interpretating of natural splines coefficients for time series   Hayssam [guest]
  • [BioC] LIMMA/VOOM: Using and Interpretating of natural splines coefficients for time series   Ryan C. Thompson
    • [BioC] LIMMA/VOOM: Using and Interpretating of natural splines coefficients for time series   Sam
      • [BioC] LIMMA/VOOM: Using and Interpretating of natural splines coefficients for time series   Ryan
• [BioC] matching Entrez-IDs to Affy probesets using biomaRt   Naomi Altman
  • [BioC] matching Entrez-IDs to Affy probesets using biomaRt   Marc Carlson
• [BioC] creating contrast matrix (limma) for two factorial in R   Ryan M Ghan
  • [BioC] creating contrast matrix (limma) for two factorial in R   Ryan
    • [BioC] creating contrast matrix (limma) for two factorial in R   Ryan M Ghan
• [BioC] strsplit   minni [guest]
  • [BioC] strsplit   Aliaksei Holik
• [BioC] pathview with tomato and minor species   Luo Weijun
• [BioC] flowviz   Mike
  • [BioC] flowviz   Mike
    • [BioC] flowviz   Mike
• [BioC] Problem retrieving dN/dS from Biomart   Marcus Goldberg
  • [BioC] Problem retrieving dN/dS from Biomart   James W. MacDonald
• [BioC] Error in getAmigoTree (RamiGO package)   suzy.stiegelmeyer at syngenta.com
  • [BioC] Error in getAmigoTree (RamiGO package)   Dan Tenenbaum
    • [BioC] Error in getAmigoTree (RamiGO package)   suzy.stiegelmeyer at syngenta.com
• [BioC] overlap regions between two GRanges (or GRangesList)   Hervé Pagès
  • [BioC] overlap regions between two GRanges (or GRangesList)   Zhao, Shanrong [JRDUS]
    • [BioC] overlap regions between two GRanges (or GRangesList)   Cook, Malcolm
  • [BioC] overlap regions between two GRanges (or GRangesList)   Hervé Pagès
    • [BioC] overlap regions between two GRanges (or GRangesList)   Hervé Pagès
  • [BioC] overlap regions between two GRanges (or GRangesList)   Hervé Pagès
• [BioC] Deseq2-help   Mubarak hussain Syed
  • [BioC] Deseq2-help   Michael Love
• [BioC] Deseq-2 help   Mubarak hussain Syed
  • [BioC] Deseq-2 help   Michael Love
• [BioC] back into the data frame   minni [guest]
• [BioC] package 'impute' is not available (for R version 3.0.2)   Jerry Cholo
  • [BioC] package 'impute' is not available (for R version 3.0.2)   Levi Waldron
  • [BioC] package 'impute' is not available (for R version 3.0.2)   Dan Tenenbaum
• [BioC] DESeq2: Error from the generic function 'plotMA' defined in package 'BiocGenerics'   Michael Love
  • [BioC] DESeq2: Error from the generic function 'plotMA' defined in package 'BiocGenerics'   David T. Auble
• [BioC] FW: using DESeq2 with multi factor data   solgakar at bi.technion.ac.il
• [BioC] DESeq2 extracting results in version >= 1.3 (was: "using DESeq2 with multi factor data")   Michael Love
  • [BioC] DESeq2 extracting results in version >= 1.3 (was: "using DESeq2 with multi factor data")   Michael Love
    • [BioC] DESeq2 extracting results in version >= 1.3 (was: "using DESeq2 with multi factor data")   Karen Chait
    • [BioC] DESeq2 extracting results in version >= 1.3 (was: "using DESeq2 with multi factor data")   Michael Love
• [BioC] Job: Bioinformatician -- Core facility DBM, Basel, Switzerland   Robert Ivanek
• [BioC] KEGG & hyperGTest: an example?   Muhammad Javed
  • [BioC] KEGG & hyperGTest: an example?   Marc Carlson
• [BioC] vmatchPattern   Richard Dannebaum [guest]
  • [BioC] vmatchPattern   Hervé Pagès
• [BioC] Surrogate Variable Analysis   Jerry Cholo
  • [BioC] Surrogate Variable Analysis   Jeff Leek
    • [BioC] Surrogate Variable Analysis   Wu, Di
• [BioC] Error message after mass5calls command MAS5.0 absolute detection   amit kumar subudhi
  • [BioC] Error message after mass5calls command MAS5.0 absolute detection   James W. MacDonald
    • [BioC] Error message after mass5calls command MAS5.0 absolute detection   cstrato
      • [BioC] Error message after mass5calls command MAS5.0 absolute detection   amit kumar subudhi
      • [BioC] Error message after mass5calls command MAS5.0 absolute detection   cstrato
• [BioC] Job: Bioinformatics Postdoc Position at the IMB, Mainz   Kathi Zarnack
• [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Magda Price [guest]
  • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Steve Lianoglou
    • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Magda Price
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   James W. MacDonald
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Magda Price
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   James W. MacDonald
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Magda Price
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   James W. MacDonald
      • [BioC] ComBat: 3 adjustment variables & continuous adjustment variables   Magda Price
• [BioC] Is there any package for meta eqtl?   Fabrice Tourre
  • [BioC] Is there any package for meta eqtl?   Vincent Carey
• [BioC] TopGo package   Qian Wang
  • [BioC] TopGo package   Dan Tenenbaum
  • [BioC] TopGo package   Dan Tenenbaum
    • [BioC] TopGo package   Qian Wang
      • [BioC] TopGo package   Dan Tenenbaum
      • [BioC] TopGo package   Adrian Alexa
• [BioC] recommend package for exon array analysis   Dli [guest]
  • [BioC] recommend package for exon array analysis   James W. MacDonald
  • [BioC] recommend package for exon array analysis   Paul Geeleher
    • [BioC] recommend package for exon array analysis   Daofeng Li
• [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   Tim Smith
  • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   James W. MacDonald
    • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   Tim Smith
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   James W. MacDonald
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   Tim Smith
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   James W. MacDonald
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   Tim Smith
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   James W. MacDonald
      • [BioC] Genes annotated to GO:0031281 using org.Hs.eg.db   Tim Smith
• [BioC] tagwise parameters for negative binomial distribution in edgeR   Davide Cittaro
  • [BioC] tagwise parameters for negative binomial distribution in edgeR   Yunshun Chen
  • [BioC] tagwise parameters for negative binomial distribution in edgeR   Gordon K Smyth
    • [BioC] tagwise parameters for negative binomial distribution in edgeR   Mark Robinson
      • [BioC] tagwise parameters for negative binomial distribution in edgeR   Davide Cittaro
      • [BioC] tagwise parameters for negative binomial distribution in edgeR   Ina Hoeschele
      • [BioC] tagwise parameters for negative binomial distribution in edgeR   Ryan C. Thompson
    • [BioC] tagwise parameters for negative binomial distribution in edgeR   Davide Cittaro
      • [BioC] tagwise parameters for negative binomial distribution in edgeR   Gordon K Smyth
      • [BioC] tagwise parameters for negative binomial distribution in edgeR   Davide Cittaro
• [BioC] GOStats: summary hyperGTest, count and size   Christine Gläßer
  • [BioC] GOStats: summary hyperGTest, count and size   Marc Carlson
  • [BioC] GOStats: summary hyperGTest, count and size   Christine Gläßer
  • [BioC] GOStats: summary hyperGTest, count and size   Christine Gläßer
• [BioC] Export mzML via mzR or other bioconductor packages   Jian [guest]
• [BioC] cummeRbund csHeatmap error   Igor Dolgalev [guest]
• [BioC] Version 1.10 of spade appears to be non-compatible with Cytoscape 2.8.x   John Quinn [guest]
  • [BioC] Version 1.10 of spade appears to be non-compatible with Cytoscape 2.8.x   Michael Linderman
• [BioC] ComBat: 2 adjustment variables & continuous adjustment variables   Magda Price
• [BioC] Orthogonal regression (edgeR, DESeq, limma or others)?   Panos Bolan
  • [BioC] Orthogonal regression (edgeR, DESeq, limma or others)?   Gordon K Smyth
• [BioC] DiffBind (Please add me to the Dropbox containing the vignette data)   Rory Stark
• [BioC] data process before overlap analysis with the DiffBind   Rory Stark
• [BioC] Have I extracted the right data with DiffBind?   Rory Stark
• [BioC] alternative for drawtext function in EBImage?   Djordje Bajic [guest]
  • [BioC] alternative for drawtext function in EBImage?   Joseph Barry
    • [BioC] alternative for drawtext function in EBImage?   Djordje Bajic
      • [BioC] alternative for drawtext function in EBImage?   Andrzej Oleś
      • [BioC] alternative for drawtext function in EBImage?   Joseph Barry
• [BioC] Heatmaps for EdgeR   Eleanor Su
  • [BioC] Heatmaps for EdgeR   Steve Lianoglou
    • [BioC] Heatmaps for EdgeR   Steve Lianoglou
      • [BioC] Heatmaps for EdgeR   Eleanor Su
      • [BioC] Heatmaps for EdgeR   Steve Lianoglou
• [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
  • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Gordon K Smyth
    • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Gordon K Smyth
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Gordon K Smyth
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Gordon K Smyth
      • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
    • [BioC] edgeR estimateGLMCommonDisp Error on RNA analysis   Justin Jeyakani (GIS)
• [BioC] looking for GRanges ggply like ddply   Ido Tamir
  • [BioC] looking for GRanges ggply like ddply   Michael Lawrence
    • [BioC] looking for GRanges ggply like ddply   Steve Lianoglou
      • [BioC] looking for GRanges ggply like ddply   Michael Lawrence
      • [BioC] looking for GRanges ggply like ddply   Steve Lianoglou
• [BioC] Bioconductor GSoC projects: DEADLINE TODAY   Michael Lawrence
• [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   rubi [guest]
  • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Michael Lawrence
    • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Cook, Malcolm
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Michael Lawrence
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   nimrod.rubinstein
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Michael Lawrence
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   nimrod.rubinstein
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Michael Lawrence
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   nimrod.rubinstein
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Cook, Malcolm
      • [BioC] Obtain overlap coordinates in GenomicRanges findSpliceOverlaps   Cook, Malcolm
• [BioC] Technical Replicates in EdgeR   Neha Mehta
  • [BioC] Technical Replicates in EdgeR   Ryan C. Thompson
• [BioC] Question about working with GRanges objects   Jeremy Ng
  • [BioC] Question about working with GRanges objects   Steve Lianoglou
  • [BioC] Question about working with GRanges objects   Michael Lawrence
    • [BioC] Question about working with GRanges objects   Jeremy Ng
• [BioC] Microarray data analysis   Prabhakar [guest]
  • [BioC] Microarray data analysis   prabhakar ghorpade
    • [BioC] Microarray data analysis   Sean Davis
      • [BioC] Microarray data analysis   Levi Waldron
      • [BioC] Microarray data analysis   prabhakar ghorpade
      • [BioC] Microarray data analysis   Steve Lianoglou
      • [BioC] Microarray data analysis   Levi Waldron
      • [BioC] Microarray data analysis   prabhakar ghorpade
      • [BioC] Microarray data analysis   Sean Davis
  • [BioC] Microarray data analysis   Steve Lianoglou
  • [BioC] Microarray data analysis   Gordon K Smyth
• [BioC] SomaticSignatures   hasif [guest]
  • [BioC] SomaticSignatures   Steve Lianoglou
    • [BioC] SomaticSignatures   Julian Gehring
    • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Huma Asif
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Martin Morgan
      • [BioC] SomaticSignatures   Huma Asif
      • [BioC] SomaticSignatures   Vincent Carey
      • [BioC] SomaticSignatures   Martin Morgan
      • [BioC] SomaticSignatures   Huma Asif
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Dan Tenenbaum
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Dan Tenenbaum
      • [BioC] SomaticSignatures   Dan Tenenbaum
      • [BioC] SomaticSignatures   Dan Tenenbaum
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Dan Tenenbaum
      • [BioC] SomaticSignatures   Steve Lianoglou
      • [BioC] SomaticSignatures   Huma Asif
      • [BioC] SomaticSignatures   Huma Asif
      • [BioC] SomaticSignatures   Martin Morgan
      • [BioC] SomaticSignatures   Vincent Carey
• [BioC] Library loading problem   prabhakar ghorpade
  • [BioC] Library loading problem   Dan Tenenbaum
    • [BioC] Library loading problem   prabhakar ghorpade
      • [BioC] Library loading problem   Steve Lianoglou
• [BioC] Is there solution to offline running Bioconductor limma   prabhakar ghorpade
  • [BioC] Is there solution to offline running Bioconductor limma   Dan Tenenbaum
• [BioC] Use of non-exported `clone` function from GenomicRange package   Peter Hickey
  • [BioC] Use of non-exported `clone` function from GenomicRange package   Michael Lawrence
    • [BioC] Use of non-exported `clone` function from GenomicRange package   Peter Hickey
      • [BioC] Use of non-exported `clone` function from GenomicRange package   Steve Lianoglou
• [BioC] Handingly outliers with voom [was: tagwise parameters for negative binomial in edgeR]   Gordon K Smyth
• [BioC] The \"retain\" parameter in quality assessment of package PROcess   Yanqing [guest]
  • [BioC] The \"retain\" parameter in quality assessment of package PROcess   Yanqing Hu
• [BioC] Data file request   prabhakar ghorpade
  • [BioC] Data file request   Steve Lianoglou
    • [BioC] Data file request   zeynep özkeserli
• [BioC] List all alignments in Biostrings   Alpesh Querer
  • [BioC] List all alignments in Biostrings   Hervé Pagès
    • [BioC] List all alignments in Biostrings   Alpesh Querer
      • [BioC] List all alignments in Biostrings   Hervé Pagès
• [BioC] To get expression data from GEO   Jerry Cholo
  • [BioC] To get expression data from GEO   vegardny
• [BioC] make.cdf.package Error in copySubstitute   matthew vitalone
  • [BioC] make.cdf.package Error in copySubstitute   James W. MacDonald
    • [BioC] make.cdf.package Error in copySubstitute   cstrato
• [BioC] problem with EdgeR script   Jim Tepperman [guest]
  • [BioC] problem with EdgeR script   Ryan
• [BioC] problem installing XML   Anthony Bosco [guest]
  • [BioC] problem installing XML   James W. MacDonald
    • [BioC] problem installing XML   Anthony Bosco
• [BioC] DESeq2 - experimental design   Michael Love
  • [BioC] DESeq2 - experimental design   Claudia Pommerenke
  • [BioC] DESeq2 - experimental design   Claudia Pommerenke
  • [BioC] DESeq2 - experimental design   Michael Love
• [BioC] preparing sequencing data for use with anota   Nils Grabole [guest]
  • [BioC] preparing sequencing data for use with anota   Ola Larsson
• [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Julian Gehring
  • [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Tengfei Yin
    • [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Tengfei Yin
      • [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Julian Gehring
      • [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Tengfei Yin
      • [BioC] ggbio: Separating lines between chromosomes with plotGrandLinear   Julian Gehring
• [BioC] rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA   Stefanie Busch [guest]
  • [BioC] rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA   James W. MacDonald
    • [BioC] rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA   James W. MacDonald
• [BioC] Plotting segment of Granges intervals   Radhouane Aniba
  • [BioC] Plotting segment of Granges intervals   Tengfei Yin
• [BioC] edgeR GLM to adjust for batch effect   Ryan Basom [guest]
  • [BioC] edgeR GLM to adjust for batch effect   Ryan C. Thompson
    • [BioC] edgeR GLM to adjust for batch effect   Ryan Basom
      • [BioC] edgeR GLM to adjust for batch effect   Ryan C. Thompson
• [BioC] Question on Gviz   Hahne, Florian
• [BioC] crlmm problem   Matthias Arnold
• [BioC] pdInfoBuilder - problem installing the annotation package   Tommaso Raffaello
  • [BioC] pdInfoBuilder - problem installing the annotation package   Benilton Carvalho
    • [BioC] pdInfoBuilder - problem installing the annotation package   James W. MacDonald
      • [BioC] pdInfoBuilder - problem installing the annotation package   Tommaso Raffaello
• [BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error   Sylvain Foisy Ph. D.
  • [BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error   Nicolas Delhomme
  • [BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error   Nicolas Delhomme
    • [BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error   Sylvain Foisy Ph. D.
      • [BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error   Nicolas Delhomme
• [BioC] Starr package: cmarrt.ma error   Zhu, Lihua (Julie)
• [BioC] DESeq2 multiple factors nested design   Isobel [guest]
  • [BioC] DESeq2 multiple factors nested design   Michael Love
    • [BioC] DESeq2 multiple factors nested design   Michael Love
      • [BioC] DESeq2 multiple factors nested design   Michael Love
• [BioC] problem with makeGOGraph function   Samuel Rochette [guest]
  • [BioC] problem with makeGOGraph function   James W. MacDonald
    • [BioC] RE : problem with makeGOGraph function   Samuel Rochette
      • [BioC] RE : problem with makeGOGraph function   James W. MacDonald
      • [BioC] RE : RE : problem with makeGOGraph function   Samuel Rochette
      • [BioC] RE : RE : problem with makeGOGraph function   James W. MacDonald
• [BioC] CellMix package use with own data matrix   Riba Michela
  • [BioC] CellMix package use with own data matrix   Renaud Gaujoux
• [BioC] .CEL file   prabhakar ghorpade
  • [BioC] .CEL file   James W. MacDonald
    • [BioC] .CEL file   prabhakar ghorpade
      • [BioC] .CEL file   James W. MacDonald
• [BioC] [phenoTest package]: gsea.kegg error with absVals parameter   Kostas Kerkentzes
• [BioC] rtracklayer connect problems   Michael Lawrence
• [BioC] time course differential analysis - design matrix   Agata [guest]
  • [BioC] time course differential analysis - design matrix   James W. MacDonald
• [BioC] Problem with geneAnswers, Reactome and some converted affy IDs   Ulrik Stervbo
• [BioC] fasta biostrings bioconductor   DNAStringSet Error Biostrings in R [guest]
  • [BioC] fasta biostrings bioconductor   Cook, Malcolm
  • [BioC] fasta biostrings bioconductor   Martin Morgan
    • [BioC] fasta biostrings bioconductor   Ivan Gregoretti
  • [BioC] fasta biostrings bioconductor   Hervé Pagès
• [BioC] MEDIPS.createSet error   Vining, Kelly
  • [BioC] MEDIPS.createSet error   Lukas Chavez
    • [BioC] MEDIPS.createSet error   Vining, Kelly
      • [BioC] MEDIPS.createSet error   Steve Lianoglou
      • [BioC] MEDIPS.createSet error   Vining, Kelly
      • [BioC] MEDIPS.createSet error   Steve Lianoglou
• [BioC] Cannot find the package created by pdInfoBuilder package   dhivya [guest]
  • [BioC] Cannot find the package created by pdInfoBuilder package   Dan Tenenbaum
    • [BioC] Cannot find the package created by pdInfoBuilder package   dhivya arasappan
      • [BioC] Cannot find the package created by pdInfoBuilder package   Benilton Carvalho
• [BioC] plotMA {limma} wrong xlab - a bug?   Yue Li
  • [BioC] plotMA {limma} wrong xlab - a bug?   James W. MacDonald
    • [BioC] plotMA {limma} wrong xlab - a bug?   Yue Li
    • [BioC] plotMA {limma} wrong xlab - a bug?   Yue Li
      • [BioC] plotMA {limma} wrong xlab - a bug?   James W. MacDonald
      • [BioC] plotMA {limma} wrong xlab - a bug?   Yue Li
      • [BioC] plotMA {limma} wrong xlab - a bug?   Yue Li
• [BioC] Using \'spliceIndex\' function from \'annmap\' package: How do I know what \'ids\' should be?   Heather [guest]
• [BioC] Most efficient way to compute width of overlap of multiple features   Michael Lawrence
  • [BioC] Most efficient way to compute width of overlap of multiple features   Michael Lawrence
    • [BioC] Most efficient way to compute width of overlap of multiple features   Vince S. Buffalo
• [BioC] Any COG enrichment tools?   Bernardo Bello
• [BioC] DEXSeq update results change   Marco Marconi
  • [BioC] DEXSeq update results change   Alejandro Reyes
• [BioC] Computing normalized counts for exons in edgeR   Nick N
  • [BioC] Computing normalized counts for exons in edgeR   Ryan
  • [BioC] Computing normalized counts for exons in edgeR   Wei Shi
• [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Hervé Pagès
  • [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Hervé Pagès
    • [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Hervé Pagès
      • [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Hervé Pagès
      • [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Niu, Liang (NIH/NIEHS) [E]
      • [BioC] A question about the function readGAlignmentPairs in GenomicRnages package   Hervé Pagès
• [BioC] Data Analysis for Genomics, free HarvardX course, starts April 7   Michael Love
• [BioC] Reading MAGE-ML cdf into bioconductor for limma in R v. 3.0.2   Ben Temperton [guest]
  • [BioC] Reading MAGE-ML cdf into bioconductor for limma in R v. 3.0.2   James W. MacDonald
• [BioC] views on Rle using GRanges object   Michael Lawrence
  • [BioC] views on Rle using GRanges object   Hervé Pagès
• [BioC] Join expression values of replicas in edgeR   María Jesús García
• [BioC] Problem with GDS2eSet   BEN HAMDA Cherif
  • [BioC] Problem with GDS2eSet   Sean Davis
• [BioC] Support vector regression   Paul [guest]
  • [BioC] Support vector regression   Steve Lianoglou
• [BioC] lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system   Franz-Josef Müller [guest]
• [BioC] Running the GSEA algorithm   Enrico Ferrero
  • [BioC] Running the GSEA algorithm   Steve Lianoglou
    • [BioC] Running the GSEA algorithm   Hooiveld, Guido
  • [BioC] Running the GSEA algorithm   Julian Gehring
    • [BioC] Running the GSEA algorithm   Steve Lianoglou
      • [BioC] Running the GSEA algorithm   Ryan
• [BioC] queries re Voom + Limma for RNA-seq data   Hooiveld, Guido
• [BioC] Difference between GDS .Cel and series.matrix.txt   BEN HAMDA Cherif
  • [BioC] Difference between GDS .Cel and series.matrix.txt   Sean Davis
• [BioC] DEXSeq dispersion trend estimation?   Ryan C. Thompson

Last message date: Mon Mar 31 23:43:18 CEST 2014
Archived on: Mon Mar 31 23:43:33 CEST 2014

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