January 2014 Archives by date
Starting: Wed Jan 1 04:02:16 CET 2014
Ending: Fri Jan 31 22:06:02 CET 2014
Messages: 605
- [BioC] gage and GO analysis
Tingzhu [guest]
- [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Zhi-Qiang Ye
- [BioC] ComBat: density.default(gamma.hat[1, ]) : 'x' contains missing values, couldn't eliminate by remove zero variance rows as suggested before
chensujun
- [BioC] gage and GO analysis
Reema Singh
- [BioC] CAMERA output to Neutral Monoisotopic Mass
Charles Determan Jr
- [BioC] edgeR complex partial multifactorial design
Gordon K Smyth
- [BioC] EdgeR glm based analysis
Gordon K Smyth
- [BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Gordon K Smyth
- [BioC] Using DESeq to test for null ratios other than 1:1
Emily [guest]
- [BioC] Using EdgeR to test for null ratios other than 1:1
Emily [guest]
- [BioC] Using DESeq to test for null ratios other than 1:1
Simon Anders
- [BioC] Using UniProt.ws to retrieve protein features
David_Gomez [guest]
- [BioC] install tcltk
liyue [guest]
- [BioC] install qvalue
liyue [guest]
- [BioC] EdgeR glm based analysis
Reema Singh
- [BioC] install tcltk
James W. MacDonald
- [BioC] install qvalue
Dan Tenenbaum
- [BioC] RCircos 2D track plot for a small region of genome
Mark Carty [guest]
- [BioC] RCircos 2D track plot for a small region of genome
Dan Tenenbaum
- [BioC] install qvalue
Dan Tenenbaum
- [BioC] Using EdgeR to test for null ratios other than 1:1
Gordon K Smyth
- [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Hervé Pagès
- [BioC] EdgeR glm based analysis
Gordon K Smyth
- [BioC] EdgeR glm based analysis
Reema Singh
- [BioC] which one should I choose in DEseq
liyue [guest]
- [BioC] which one should I choose in DEGseq
liyue [guest]
- [BioC] install qvalue
Martin Morgan
- [BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Zhi-Qiang Ye
- [BioC] which one should I choose in DEseq
Simon Anders
- [BioC] makeSPIAdata
David Price
- [BioC] makeSPIAdata
Tarca, Adi
- [BioC] Parse sequences so they align properly
Josh Banta [guest]
- [BioC] job: head of core facility bioinformatics (Mainz/Germany)
Holger Klein
- [BioC] FDR and Estimated Fragment length
Ryan
- [BioC] Error using oligo package with Affymetrix Arabidopsis Gene ST1.0 array data: paCalls() returns error 'vector would be too long'
Peter Crisp
- [BioC] Parse sequences so they align properly
Hervé Pagès
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Joseph Shaw [guest]
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Joseph Shaw [guest]
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Ryan
- [BioC] Inquiry about lumiT function
Neagu Matei Stefan [guest]
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Joseph Shaw
- [BioC] Parse sequences so they align properly
Joshua Banta
- [BioC] Parse sequences so they align properly
Martin Morgan
- [BioC] Parse sequences so they align properly
Hervé Pagès
- [BioC] Inquiry about lumiT function
Pan Du
- [BioC] Parse sequences so they align properly
Hervé Pagès
- [BioC] Error in dispersionPlot using cummeRbund
Nancy [guest]
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Gordon K Smyth
- [BioC] Help needed: extracting raw intensity values from Affy
shweta bagewadi
- [BioC] Help needed: extracting raw intensity values from Affy
Assa Yeroslaviz
- [BioC] [MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
김종환
- [BioC] Help needed: extracting raw intensity values from Affy
shweta bagewadi
- [BioC] miRBase
Shantanu Karkare [guest]
- [BioC] Fwd: GWASTools
Stephanie M. Gogarten
- [BioC] miRBase
Dan Tenenbaum
- [BioC] Error in dispersionPlot using cummeRbund
Loyal A. Goff
- [BioC] [MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Lukas Chavez
- [BioC] EdgeR multi-factor testing questions
Yanzhu [guest]
- [BioC] Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital, Boston, MA, USA
Wittner, Ben, Ph.D.
- [BioC] Most efficient way to compute width of overlap of multiple features
Vince S. Buffalo
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Joseph Shaw
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Gordon K Smyth
- [BioC] ensemblVEP, variant_effect_predictor versions and release schedule
Thomas Sandmann
- [BioC] [MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
김종환
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Noa Henig
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Michael Love
- [BioC] Extracting protein sequence associated to UCSC transcript id
rcaloger
- [BioC] Extracting protein sequence associated to UCSC transcript id
Michael Lawrence
- [BioC] Most efficient way to compute width of overlap of multiple features
Charles Berry
- [BioC] Most efficient way to compute width of overlap of multiple features
Michael Lawrence
- [BioC] Normalizing Affy Almac Xcel Array Data from CEL files
Wei Chen [guest]
- [BioC] Normalizing Affy Almac Xcel Array Data from CEL files
James W. MacDonald
- [BioC] Most efficient way to compute width of overlap of multiple features
Charles Berry
- [BioC] Most efficient way to compute width of overlap of multiple features
Michael Lawrence
- [BioC] Normalizing Affy Almac Xcel Array Data from CEL files
cstrato
- [BioC] Gviz UcscTrack error
Anna Sawicka [guest]
- [BioC] Problem with BAM header in GAlignments
Taylor, Sean D
- [BioC] Problem with BAM header in GAlignments
Taylor, Sean D
- [BioC] Problem with BAM header in GAlignments
Martin Morgan
- [BioC] Problem with BAM header in GAlignments
Taylor, Sean D
- [BioC] EdgeR multi-factor testing questions
Gordon K Smyth
- [BioC] Problem with BAM header in GAlignments
Martin Morgan
- [BioC] Problem with BAM header in GAlignments
Taylor, Sean D
- [BioC] Design/Contrast for Two-Channel Experimental Setup
Joseph Shaw
- [BioC] Retrieving Adjusted Individual Channel Intensities
Joseph Shaw [guest]
- [BioC] Question about best analysis method for a complex array expriment design
Agnes Paquet
- [BioC] miRBase
Shantanu Karkare
- [BioC] EximiR - Limma - miRCURY LNA - Exiqon
Paolo Kunderfranco
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Noa Henig
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Simon Anders
- EdgeR multi-factâ or testing questions
Yanzhu [guest]
- [BioC] VCF as custom variant annotation database
Francesco Lescai
- [BioC] Retrieving Adjusted Individual Channel Intensities
James W. MacDonald
- [BioC] Extracting protein sequence associated to UCSC transcript id
rcaloger
- [BioC] EdgeR multi-factor testing question
Yanzhu [guest]
- [BioC] BiocStyle short header
Andrzej Oleś
- [BioC] Extracting protein sequence associated to UCSC transcript id
Michael Lawrence
- [BioC] VCF as custom variant annotation database
Valerie Obenchain
- [BioC] Querying a HDF5 database from R
James Mahon [guest]
- [BioC] BiocStyle short header
Martin Morgan
- [BioC] Extracting protein sequence associated to UCSC transcript id
rcaloger
- [BioC] Extracting protein sequence associated to UCSC transcript id
Hervé Pagès
- [BioC] Reading by column
Hajas, Wayne
- [BioC] BiocStyle short header
Bernd Fischer
- [BioC] Extracting protein sequence associated to UCSC transcript id
Marc Carlson
- [BioC] Question about best analysis method for a complex array experiment design
Gordon K Smyth
- [BioC] package installation
array chip
- [BioC] package installation
James W. MacDonald
- [BioC] Extracting protein sequence associated to UCSC transcript id
Michael Lawrence
- [BioC] Multi-level experiments
Yu Cai [guest]
- [BioC] Multi-level experiments
Dario Strbenac
- [BioC] Gviz UcscTrack error
Hahne, Florian
- [BioC] Gviz UcscTrack error
Anna Sawicka
- [BioC] Extracting protein sequence associated to UCSC transcript id
rcaloger
- [BioC] diffbind question : bSubControl with DEseq
Rory Stark
- [BioC] DESeq nbinomGLMTest specific comparisons
James Floyd
- [BioC] VCF as custom variant annotation database
Francesco Lescai
- [BioC] Extracting protein sequence associated to UCSC transcript id
James W. MacDonald
- [BioC] GLM common and trended dispersion EdgeR.
Reema Singh
- [BioC] Extracting protein sequence associated to UCSC transcript id
rcaloger
- [BioC] annotation of a probe in hgu133plus2
Mayte Suarez-Farinas
- [BioC] Normalizing Affy Almac Xcel Array Data from CEL files
Dr Wei Chen
- [BioC] annotation of a probe in hgu133plus2
James W. MacDonald
- [BioC] Normalizing Affy Almac Xcel Array Data from CEL files
James W. MacDonald
- [BioC] Annotate package not working
Ryan C. Thompson
- [BioC] Annotate package not working
Dan Tenenbaum
- [BioC] Annotate package not working
James W. MacDonald
- [BioC] Annotate package not working
Ryan C. Thompson
- [BioC] annotation of a probe in hgu133plus2
James W. MacDonald
- [BioC] GLM common and trended dispersion EdgeR.
Ryan C. Thompson
- [BioC] Annotate package not working
Dan Tenenbaum
- [BioC] EdgeR multi-factor testing question
Gordon K Smyth
- [BioC] Annotate package not working
Ryan C. Thompson
- [BioC] Annotate package not working
Martin Morgan
- [BioC] GLM common and trended dispersion EdgeR.
Reema Singh
- [BioC] Best way to remove noise from dataset.
Fenton Christopher Graham
- [BioC] Best way to remove noise from dataset.
Arnar Flatberg
- [BioC] DEXSeq analysis for paired samples
Philip Jonsson
- [BioC] R pathview and mouse
Luo Weijun
- [BioC] biomaRt: retrieve exon sequence, start and end positions
Tim Smith
- [BioC] biomaRt: retrieve exon sequence, start and end positions
Steffen Durinck
- [BioC] limma - normalizeBetweenArrays function
MIKE STARKEY
- [BioC] Annotate package not working
Ryan C. Thompson
- [BioC] DESeq nbinomGLMTest specific comparisons
Ryan C. Thompson
- [BioC] Q-values way smaller than P-values! Is that kosher?
Joshua Banta
- [BioC] Q-values way smaller than P-values! Is that kosher?
Joshua Banta [guest]
- [BioC] DEXSeq analysis for paired samples
Simon Anders
- [BioC] Extracting protein sequence associated to UCSC transcript id
Marc Carlson
- [BioC] Extracting protein sequence associated to UCSC transcript id
Marc Carlson
- [BioC] GLM common and trended dispersion EdgeR
Gordon K Smyth
- [BioC] Error in dispersionPlot using cummeRbund
Yanxiang Shi
- [BioC] GenomicFeatures support for UCSC Microbial Genome Browser
Olusegun Oshota [guest]
- [BioC] Q-values way smaller than P-values! Is that kosher?
Michael Love
- [BioC] EdgeR design question?
joseph
- [BioC] limma - normalizeBetweenArrays function
Gordon K Smyth
- [BioC] Q-values way smaller than P-values! Is that kosher?
Gordon K Smyth
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Noa Henig
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Michael Love
- [BioC] Q-values way smaller than P-values! Is that kosher?
Joshua Banta
- [BioC] annotation of a probe in hgu133plus2
Mayte Suarez-Farinas
- [BioC] Q-values way smaller than P-values! Is that kosher?
Tim Triche, Jr.
- [BioC] 'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories
Barry Garchow
- [BioC] Q-values way smaller than P-values! Is that kosher?
Tim Triche, Jr.
- [BioC] 'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories
cstrato
- [BioC] EdgeR design question?
Gordon K Smyth
- [BioC] Q-values way smaller than P-values! Is that kosher?
Gordon K Smyth
- [BioC] question edgeR multifactorial design
David Rengel
- [BioC] An introductory course to RNA-seq at MBC Via Nizza 52, Torino, Italy, 25-27 March 2014
rcaloger
- [BioC] [job offer phd position]
Sonja Haenzelmann [guest]
- [BioC] DESeq nbinomGLMTest specific comparisons
James Floyd
- [BioC] EdgeR design question?
joseph
- [BioC] ensemblVEP, variant_effect_predictor versions and release schedule
Valerie Obenchain
- [BioC] ensemblVEP, variant_effect_predictor versions and release schedule
Valerie Obenchain
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina Fontanez [guest]
- [BioC] 'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories
Barry Garchow
- [BioC] DESeq: multi-factors testing questions
Yanzhu [guest]
- [BioC] 'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories
cstrato
- [BioC] AllelicImbalance with VCFs?
Tim Triche, Jr.
- [BioC] DEseq2 metagenomic analysis without replicates
Steve Lianoglou
- [BioC] using frma and brainarray cdf on exon arrays
Ty Thomson
- [BioC] using frma and brainarray cdf on exon arrays
Matthew McCall
- [BioC] DEseq2 metagenomic analysis without replicates
Simon Anders
- [BioC] using frma and brainarray cdf on exon arrays
Ty Thomson
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] EdgeR design question?
Gordon K Smyth
- [BioC] DEseq2 metagenomic analysis without replicates
Simon Anders
- [BioC] EdgeR for proteomics data
Phinney, Brett
- [BioC] Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Thornton, Matthew
- [BioC] multiple groups time course RNA Seq LIMMA
Riba Michela
- [BioC] AllelicImbalance with VCFs?
Jesper Robert Gadin
- [BioC] using frma and brainarray cdf on exon arrays
Steve Piccolo
- [BioC] extracting transcripts
Jahn Davik
- [BioC] using frma and brainarray cdf on exon arrays
Ty Thomson
- [BioC] using frma and brainarray cdf on exon arrays
Steve Piccolo
- [BioC] Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
James W. MacDonald
- [BioC] using frma and brainarray cdf on exon arrays
Ty Thomson
- [BioC] extracting transcripts
James W. MacDonald
- [BioC] retrieving LD between two known SNPs with rsID
Francesco Lescai
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Michael Love
- [BioC] EdgeR for proteomics data
Ryan
- [BioC] ChIPpeakAnno: TSS at - strand
Zhu, Lihua (Julie)
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] DEseq2 metagenomic analysis without replicates
Simon Anders
- [BioC] unable to install biocLite or BiocInstaller
Naomi Altman
- [BioC] using frma and brainarray cdf on exon arrays
Benilton Carvalho
- [BioC] unable to install biocLite or BiocInstaller
Benilton Carvalho
- [BioC] estimating size factors in DESeq produces warnings
Assa Yeroslaviz
- [BioC] unable to install biocLite or BiocInstaller
Vincent Carey
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] ChIPpeakAnno: TSS at - strand
Zhu, Lihua (Julie)
- [BioC] unable to install biocLite or BiocInstaller
Steve Lianoglou
- [BioC] using frma and brainarray cdf on exon arrays
Matthew McCall
- [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
Abhishek Pratap
- [BioC] retrieving LD between two known SNPs with rsID
Valerie Obenchain
- [BioC] estimating size factors in DESeq produces warnings
Simon Anders
- [BioC] GLM common and trended dispersion EdgeR
Reema Singh
- [BioC] AllelicImbalance with VCFs?
Jesper Robert Gadin
- [BioC] oligo read.celfiles() error
Guest [guest]
- [BioC] I need help making a dcf seed file to encapsulate a genome assembly im using.
Hervé Pagès
- [BioC] Reading by column
Nathaniel Hayden
- [BioC] oligo read.celfiles() error
Kasoji, Manjula (NIH/NCI) [C]
- [BioC] I need help making a dcf seed file to encapsulate a genome assembly im using.
ashteyma at andrew.cmu.edu
- [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
Stephanie M. Gogarten
- [BioC] Reading by column
Hajas, Wayne
- [BioC] question edgeR multifactorial design
Gordon K Smyth
- [BioC] multiple groups time course RNA Seq LIMMA
Gordon K Smyth
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
Lei Huang [guest]
- [BioC] ChIPpeakAnno: TSS at - strand
Yu, Guangchuang
- [BioC] multiple groups time course RNA Seq LIMMA
Riba Michela
- [BioC] makeTranscriptDbFromUCSC
Georg Otto
- [BioC] [MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Pierre Lindenbaum
- [BioC] ChIPpeakAnno: TSS at - strand
Ou, Jianhong
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
James W. MacDonald
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
cstrato
- [BioC] DESeq2 high fold change values for comparison of samples with zero counts
Michael Love
- [BioC] DESeq: multi-factors testing questions
Michael Love
- [BioC] AllelicImbalance with VCFs?
Valerie Obenchain
- [BioC] makeTranscriptDbFromUCSC() error
Chris Cabanski
- [BioC] [MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Matthias Lienhard
- [BioC] Research questions that are answered using MotifDb
T M
- [BioC] makeTranscriptDbFromUCSC() error
Chris Cabanski
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
James W. MacDonald
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
Huang, Lei [BSD] - CRI
- [BioC] Reading by column
Hajas, Wayne
- [BioC] using frma and brainarray cdf on exon arrays
Steve Piccolo
- [BioC] Find enriched GO terms, given a list of GO terms of interest and background GO terms
JJ [guest]
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
James W. MacDonald
- [BioC] finding a very large number of false positives using edgeR
Blum, Charles
- [BioC] [devteam-bioc] GenomicFeatures support for UCSC Microbial Genome Browser
Hervé Pagès
- [BioC] finding a very large number of false positives using edgeR
Steve Lianoglou
- [BioC] exomeCopy tutorial steps
Brett Spurrier
- [BioC] finding a very large number of false positives using edgeR
Blum, Charles
- [BioC] Error in dispersionPlot using cummeRbund
Yanxiang Shi
- [BioC] makeGappedAlignmentPairs for broken pairs
Ido Tamir
- [BioC] exomeCopy tutorial steps
Vincent Carey
- [BioC] exomeCopy tutorial steps
Michael Love
- [BioC] makeTranscriptDbFromUCSC
Georg Otto
- [BioC] DEseq2 metagenomic analysis without replicates
Simon Anders
- [BioC] fRMA for Gene ST arrays
maria
- [BioC] Cluster stability/robustness
Rafi [guest]
- [BioC] Cluster stability/robustness
James W. MacDonald
- [BioC] Find enriched GO terms, given a list of GO terms of interest and background GO terms
Adrian Alexa
- [BioC] biomaaRt error: Extra content at the end of the document
Hari Easwaran
- [BioC] biomaaRt error: Extra content at the end of the document
Steffen Durinck
- [BioC] finding a very large number of false positives using edgeR
Steve Lianoglou
- [BioC] biomaaRt error: Extra content at the end of the document
Hari Easwaran
- [BioC] ComBat: Error when including numerical covariates in model (numCovs)
Jordan Ramsey
- [BioC] AllelicImbalance with VCFs?
Valerie Obenchain
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] ComBat: Error when including numerical covariates in model (numCovs)
Johnson, William Evan
- [BioC] pathway analysis by SPIA using SPIA package vs graphite package
array chip
- [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
Abhishek Pratap
- [BioC] makeGappedAlignmentPairs for broken pairs
Valerie Obenchain
- [BioC] ComBat: Error when including numerical covariates in model (numCovs)
Jordan Ramsey
- [BioC] ComBat: Error when including numerical covariates in model (numCovs)
Johnson, William Evan
- [BioC] Find enriched GO terms, given a list of GO terms of interest and background GO terms
JJ Chai
- [BioC] Cluster stability/robustness
rafi A
- [BioC] Inquiries on recommended design formulae for various experiments
Yoong [guest]
- [BioC] pre-ranked GSEA within R: options?
Daniel Schmolze
- [BioC] Cluster stability/robustness
James W. MacDonald
- [BioC] DEXSeq - identical p-values for all exons in a gene
KP [guest]
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] DEXSeq - identical p-values for all exons in a gene
Steve Lianoglou
- [BioC] finding a very large number of false positives using edgeR
Gordon K Smyth
- [BioC] pre-ranked GSEA within R?
Daniel Schmolze
- [BioC] DEseq2 metagenomic analysis without replicates
Michael Love
- [BioC] DEseq2 metagenomic analysis without replicates
Michael Love
- [BioC] Can subjunc use splice sites from a reference annotation (i.e. GTF file)?
Ryan C. Thompson
- [BioC] Inquiries on recommended design formulae for various experiments
Michael Love
- [BioC] DEXSeq - identical p-values for all exons in a gene
Pillman, Katherine (Health)
- [BioC] pathway analysis by SPIA using SPIA package vs graphite package
array chip
- [BioC] DEXSeq - identical p-values for all exons in a gene
Dario Strbenac
- [BioC] DEXSeq - identical p-values for all exons in a gene
Pillman, Katherine (Health)
- [BioC] Can subjunc use splice sites from a reference annotation (i.e. GTF file)?
Wei Shi
- [BioC] DEXSeq - identical p-values for all exons in a gene
Simon Anders
- [BioC] DEXSeq - identical p-values for all exons in a gene
Simon Anders
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Garcia Manteiga Jose Manuel
- [BioC] makeGappedAlignmentPairs for broken pairs
Ido Tamir
- [BioC] DEseq2 metagenomic analysis without replicates
Simon Anders
- [BioC] pre-ranked GSEA within R?
Pekka Kohonen
- [BioC] pre-ranked GSEA within R?
Leif Väremo
- [BioC] Labeling BAM files in Cufflinks/Cuffdiff input
Sindre Lee
- [BioC] pre-ranked GSEA within R?
Pekka Kohonen
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Michael Love
- [BioC] makeGappedAlignmentPairs for broken pairs
Valerie Obenchain
- [BioC] EdgeR for proteomics data
Pekka Kohonen
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] DEseq2 metagenomic analysis without replicates
Michael Love
- [BioC] unable to install biocLite or BiocInstaller
naomi at stat.psu.edu
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] DESeq2: NA on padj column when doing bonferroni
David Rengel
- [BioC] DESeq2: NA on padj column when doing bonferroni
Kristina M Fontanez
- [BioC] DESeq2: NA on padj column when doing bonferroni
David Rengel
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Garcia Manteiga Jose Manuel
- [BioC] DESeq2: NA on padj column when doing bonferroni
Garcia Manteiga Jose Manuel
- [BioC] DESeq2: NA on padj column when doing bonferroni
Kristina M Fontanez
- [BioC] Reading by column
Bernd Fischer
- [BioC] Querying a HDF5 database from R
Bernd Fischer
- [BioC] DESeq2: NA on padj column when doing bonferroni
David Rengel
- [BioC] DESeq2: NA on padj column when doing bonferroni
Kristina M Fontanez
- [BioC] DEseq2 metagenomic analysis without replicates
Kristina M Fontanez
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Michael Love
- [BioC] DESeq2: NA on padj column when doing bonferroni
Michael Love
- [BioC] edgeR FC calculation question
Lana Schaffer
- [BioC] DESeq2: NA on padj column when doing bonferroni
David Rengel
- [BioC] Error installing development version of DESeq2
Kristina M Fontanez
- [BioC] edgeR FC calculation question
Ryan C. Thompson
- [BioC] Error installing development version of DESeq2
Dan Tenenbaum
- [BioC] Error installing development version of DESeq2
Kristina M Fontanez
- [BioC] Error installing development version of DESeq2
Steve Lianoglou
- [BioC] Error installing development version of DESeq2
Kristina M Fontanez
- [BioC] Error installing development version of DESeq2
Steve Lianoglou
- [BioC] RCytoscape: tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
Paul Shannon
- [BioC] DEseq2 metagenomic analysis without replicates
Michael Love
- [BioC] Error installing development version of DESeq2
Kristina M Fontanez
- [BioC] tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
Paul Shannon
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom
Gordon K Smyth
- [BioC] Error installing development version of DESeq2
Steve Lianoglou
- [BioC] Cluster stability/robustness
Wolfgang Huber
- [BioC] fRMA for Gene ST arrays
Matthew McCall
- [BioC] DESeq2: NA on padj column when doing bonferroni
David Rengel
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Gordon K Smyth
- [BioC] obtaining the counts after batch effect removal
Gilgi [guest]
- [BioC] Problem when trying to use \'affy\' package
Kaj Chokeshaiusaha [guest]
- [BioC] Problem with PMcorrection and Summarization
Kaj Chokeshaiusaha [guest]
- [BioC] obtaining the counts after batch effect removal
Michael Love
- [BioC] obtaining the counts after batch effect removal
Michael Love
- [BioC] IPPD model fit
Yuri Galachyants
- [BioC] DEXSeq - identical p-values for all exons in a gene
Pillman, Katherine (Health)
- [BioC] Trouble installing BiocGenerics
Andreas Leha
- [BioC] obtaining the counts after batch effect removal
Gilgi Friedlander
- [BioC] obtaining the counts after batch effect removal
Wolfgang Huber
- [BioC] obtaining the counts after batch effect removal
Gilgi Friedlander
- [BioC] DEXSeq - identical p-values for all exons in a gene
Simon Anders
- [BioC] Trouble installing BiocGenerics
Vincent Carey
- [BioC] Trouble installing BiocGenerics
Andreas Leha
- [BioC] GOstats, query between the GO set from geneIdsByCategory and the GO set from org.Ce.egGO
余淼
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Jose Garcia
- [BioC] conditional merge of duplicated rows in data.frame
Ninni Nahm [guest]
- [BioC] help with array based microRNA data analysis
Abhishek Pratap
- [BioC] help with array based microRNA data analysis
Paul Geeleher
- [BioC] pathview vectorized output?
Luo Weijun
- [BioC] conditional merge of duplicated rows in data.frame
Martin Morgan
- [BioC] help with array based microRNA data analysis
Abhishek Pratap
- [BioC] FLowClust/FLowCore
Vijay [guest]
- [BioC] GOstats, query between the GO set from geneIdsByCategory and the GO set from org.Ce.egGO
Dan Du
- [BioC] BiomaRt Ensembl RefSeq query error
Georg Otto
- [BioC] BiomaRt Ensembl RefSeq query error
Georg Otto
- [BioC] Question about quantile normalization and NA value
H at mamba.fhcrc.org
- [BioC] Problem installing BiocGenerics package
Eric Lucas [guest]
- [BioC] Error installing development version of DESeq2
Kristina M Fontanez
- [BioC] [devteam-bioc] Problem installing BiocGenerics package
Dan Tenenbaum
- [BioC] Get actual coordinates for the predicted loci
Joel RodrÃguez-Medina [guest]
- [BioC] how to extract probes for a probeset from PdInfo database?
Hooiveld, Guido
- [BioC] conditional merge of duplicated rows in data.frame
Ninni Nahm
- [BioC] [devteam-bioc] Problem installing BiocGenerics package
Eric Lucas
- [BioC] Question about quantile normalization and NA value
Steve Lianoglou
- [BioC] how to extract probes for a probeset from PdInfo database?
Wu, Di
- [BioC] how to extract probes for a probeset from PdInfo database?
Benilton Carvalho
- [BioC] Problem when trying to use \'affy\' package
James W. MacDonald
- [BioC] Voom and removing batch effect
Heather Estrella
- [BioC] Voom and removing batch effect
Ryan C. Thompson
- [BioC] how to extract probes for a probeset from PdInfo database?
Hooiveld, Guido
- [BioC] FLowClust/FLowCore
Mike
- [BioC] ChIPpeakAnno: 6-way venn diagram
Zhu, Lihua (Julie)
- [BioC] rMAT install error
周在威
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Gordon K Smyth
- [BioC] get promoter regions (bed format) of genes hg19
Ninni Nahm [guest]
- [BioC] Get actual coordinates for the predicted loci
Tom Hardcastle
- [BioC] bsmooth and bsseq for RRBS
Gilgi [guest]
- [BioC] RRBS question
Alex Gutteridge
- [BioC] Design matrix in Combat algorithm
Neagu Matei Stefan [guest]
- [BioC] A relevant petition
Vincent Detours [guest]
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Dimitra Alexopoulou
- [BioC] Question about quantile normalization and NA value
godahajime
- [BioC] maQualityPlots: cannot coerce type 'S4' to vector of type 'double'
Saket Choudhary
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Michael Love
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Dimitra Alexopoulou
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
James W. MacDonald
- [BioC] Design matrix in Combat algorithm
Johnson, William Evan
- [BioC] RRBS question
Kasper Daniel Hansen
- [BioC] Summer Internship at Genentech
Jessica Larson
- [BioC] get promoter regions (bed format) of genes hg19
Valerie Obenchain
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Jason Hackney
- [BioC] RRBS question
Alex Gutteridge
- [BioC] RRBS question
Tim Triche, Jr.
- [BioC] bsmooth and bsseq for RRBS
Tim Triche, Jr.
- [BioC] Question about quantile normalization and NA value
Steve Lianoglou
- [BioC] RRBS question
Gilgi Friedlander
- [BioC] bsmooth and bsseq for RRBS
Gilgi Friedlander
- [BioC] get promoter regions (bed format) of genes hg19
Harris A. Jaffee
- [BioC] Odd contrast; does it make statistical sense?
Ryan C. Thompson
- [BioC] BiomaRt Ensembl RefSeq query error
Davis, Wade
- [BioC] Question about quantile normalization and NA value
Gordon K Smyth
- [BioC] Question about quantile normalization and NA value
Ben Bolstad
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Jose Garcia
- [BioC] paCalls() in oligo package fails for exon arrays (Error in normalizeSingleBracketSubscript)
Maria Rodrigo-Domingo [guest]
- [BioC] Question about quantile normalization and NA value
godahajime
- [BioC] DBChIP errors
mali salmon
- [BioC] maQualityPlots: cannot coerce type 'S4' to vector of type
Agnes Paquet
- [BioC] paCalls() in oligo package fails for exon arrays (Error in normalizeSingleBracketSubscript)
Benilton Carvalho
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Dimitra Alexopoulou
- [BioC] paCalls() in oligo package fails for exon arrays (Error in normalizeSingleBracketSubscript)
Maria Rodrigo-Domingo
- [BioC] Affymetrix HTA 2 array analysis
Elena Serrano
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Gabriel Becker
- [BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion
Amanda F A Riccardi [guest]
- [BioC] Error reading imputed file using snpStats package
francesca casalino
- [BioC] Error reading imputed file using snpStats package
francesca casalino
- [BioC] Error reading imputed file using snpStats package
Vincent Carey
- [BioC] [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Jason Hackney
- [BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion
James W. MacDonald
- [BioC] Clusplot - changing cluster labels
Peterson, Leif
- [BioC] pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
Guilherme Rocha
- [BioC] BiomaRt Ensembl RefSeq query error
Georg Otto
- [BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion
James W. MacDonald
- [BioC] Agi4x44Preprocess - error on read.AgilentFE fucntion
amandafassis at usp.br
- [BioC] pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
James W. MacDonald
- [BioC] The ambiguous alignment examples in findMateAlignment don't have to be dumped
yun YAN
- [BioC] genefilter kOverA filter by range
Kristina M Fontanez
- [BioC] genefilter kOverA filter by range
James W. MacDonald
- [BioC] Error reading imputed file using snpStats package
francesca casalino
- [BioC] genefilter kOverA filter by range
Kristina M Fontanez
- [BioC] 2 issues about enriched gene sets via Roast
julie.leonard at syngenta.com
- [BioC] genefilter kOverA filter by range
James W. MacDonald
- [BioC] pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
Gordon K Smyth
- [BioC] genefilter kOverA filter by range
Kristina M Fontanez
- [BioC] beadarray: mRNA QC help
Abhishek Pratap
- [BioC] Odd contrast; does it make statistical sense?
Gordon K Smyth
- [BioC] EBSeq Results Affected By Outlying Values
Dario Strbenac
- [BioC] Follow-up: Multiple comparisons using contrast
Yoong [guest]
- [BioC] Limma design and contrast matrix question.
Thornton, Matthew
- [BioC] The ambiguous alignment examples in findMateAlignment don't have to be dumped
Hervé Pagès
- [BioC] beadarray: mRNA QC help
Levi Waldron
- [BioC] Limma design and contrast matrix question.
Dario Strbenac
- [BioC] GLM design matrix not symmetric
Michael Moore
- [BioC] Follow-up: Multiple comparisons using contrast
Michael Love
- [BioC] edgeR - common dispersion and BCV
Avinash S
- [BioC] restoring lattice-like format in flowViz?
David Ornelles [guest]
- [BioC] Odd contrast; does it make statistical sense?
Aaron Mackey
- [BioC] Odd contrast; does it make statistical sense?
Ryan
- [BioC] Odd contrast; does it make statistical sense?
Gordon K Smyth
- [BioC] beadarray: mRNA QC help
Levi Waldron
- [BioC] Limma design and contrast matrix question.
James W. MacDonald
- [BioC] 2 issues about enriched gene sets via Roast
julie.leonard at syngenta.com
- [BioC] Odd contrast; does it make statistical sense?
Aaron Mackey
- [BioC] DESeq2 pitfalls of rlog transformation
Kristina M Fontanez
- [BioC] DESeq2 pitfalls of rlog transformation
Michael Love
- [BioC] DESeq2 pitfalls of rlog transformation
Kristina M Fontanez
- [BioC] Limma design and contrast matrix question.
Thornton, Matthew
- [BioC] Limma design and contrast matrix question.
Thornton, Matthew
- [BioC] Limma design and contrast matrix question.
James W. MacDonald
- [BioC] DESeq2 pitfalls of rlog transformation
Kristina M Fontanez
- [BioC] Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
Isaac Neuhaus
- [BioC] How to use ALLR to calculate motifDistance
Ou, Jianhong
- [BioC] The ambiguous alignment examples in findMateAlignment don't have to be dumped
yun YAN
- [BioC] beadarray: mRNA QC help
Abhishek Pratap
- [BioC] The ambiguous alignment examples in findMateAlignment don't have to be dumped
Hervé Pagès
- [BioC] non-BiomaRt die
Waqasuddin Khan [guest]
- [BioC] 2 issues about enriched gene sets via Roast
Gordon K Smyth
- [BioC] 2 issues about enriched gene sets via Roast
Gordon K Smyth
- [BioC] GLM design matrix not symmetric
Gordon K Smyth
- [BioC] GLM design matrix not symmetric
Gordon K Smyth
- [BioC] ComBat error message
Ingrid Dahlman [guest]
- [BioC] non-BiomaRt die
Dan Tenenbaum
- [BioC] Odd contrast; does it make statistical sense?
Gordon K Smyth
- [BioC] Odd contrast; does it make statistical sense?
Gordon K Smyth
- [BioC] Odd contrast; does it make statistical sense?
Ryan
- [BioC] Error Using DESeq with HTSeq-Count
Xiaoyu Liang
- [BioC] Multiple comparisons: inquiries on level factors and wording used in resultsNames
Yoong [guest]
- [BioC] problem in getVarianceStabilizedData
Suparna Mitra
- [BioC] Problem when trying to use \'affy\' package
Kaj
- [BioC] Tool inqured to analysis array expression and cell line screening data
Ran [guest]
- [BioC] which dispersion to choose
Ruprecht Kathrin
- [BioC] EdgeR multi-factors testing questions
Yanzhu [guest]
- [BioC] problem in getVarianceStabilizedData
Michael Love
- [BioC] Multiple comparisons: inquiries on level factors and wording used in resultsNames
Michael Love
- [BioC] Error Using DESeq with HTSeq-Count
Michael Love
- [BioC] Error Using DESeq with HTSeq-Count
Xiaoyu Liang
- [BioC] Error Using DESeq with HTSeq-Count
Devon Ryan
- [BioC] Error Using DESeq with HTSeq-Count
Michael Love
- [BioC] Error Using DESeq with HTSeq-Count
Xiaoyu Liang
- [BioC] Problem when trying to use \'affy\' package
James W. MacDonald
- [BioC] Problem when trying to use \'affy\' package
James W. MacDonald
- [BioC] Tool inqured to analysis array expression and cell line screening data
Steve Lianoglou
- [BioC] beadarray: mRNA QC help
Abhishek Pratap
- [BioC] 2 issues about enriched gene sets via Roast
julie.leonard at syngenta.com
- [BioC] restoring lattice-like format in flowViz?
Mike
- [BioC] EdgeR multi-factors testing questions
Ryan C. Thompson
- [BioC] DEXSeq - identical p-values for all exons in a gene
Pillman, Katherine (Health)
- [BioC] problem in getVarianceStabilizedData
Suparna Mitra
- [BioC] Save top genes used in plotMDS (edgeR)
María Jesús García
- [BioC] Gviz pacakge
Hahne, Florian
- [BioC] howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
Stephane Plaisance | VIB |
- [BioC] howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
Vincent Carey
- [BioC] howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
Vincent Carey
- [BioC] howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
Vincent Carey
- [BioC] howto map HuEx-1_0-st-v2 transcript_cluster_id's to gene symbols
Jeremy Ng
- [BioC] EdgeR multi-factors testing questions
Yanzhu [guest]
- [BioC] limma and Volcano Plots
Saket Choudhary
- [BioC] FlowCore: problem with reading and writing fcs files
Maria Chikina [guest]
- [BioC] DiffBind Questions
Rory Stark
- [BioC] which dispersion to choose
Gordon K Smyth
- [BioC] Save top genes used in plotMDS (edgeR)
Gordon K Smyth
- [BioC] limma and Volcano Plots
Saket Choudhary
- [BioC] questions on edgeR package
Ming Yi
- [BioC] Multifactorial edgeR GLM design question (contrast that I should make)
Zhihao Tan
- [BioC] questions on edgeR package
Gordon K Smyth
- [BioC] questions on edgeR package
Dario Strbenac
- [BioC] questions on edgeR package
Ming Yi
- [BioC] questions on edgeR package
Ming Yi
- [BioC] DESeq2 - working with partial replicates
Avinash S
- [BioC] DESeq2 - working with partial replicates
Michael Love
- [BioC] DESeq2 - working with partial replicates
Avinash S
- [BioC] questions on edgeR package
Gordon K Smyth
- [BioC] edgeR
Jahn Davik [guest]
- [BioC] ggplot2 error
Alyaa Mahmoud
- [BioC] ggplot2 error
Alyaa Mahmoud
- [BioC] EdgeR plotSmear varied size fo de.tag points
Dave Gerrard
- [BioC] Multifactorial edgeR GLM design question (contrast that I should make)
James W. MacDonald
- [BioC] Defining the model matrix for a multi-factorial design with interactions - edgeR
Marco [guest]
- [BioC] calling aberrations after segmentation with \"copynumber\" package
Gabriele Zoppoli [guest]
- [BioC] DESeq2 - input data questions
Ming Yi
- [BioC] Multifactorial edgeR GLM design question (contrast that I should make)
Zhihao Tan
- [BioC] ggplot2 error
Steve Lianoglou
- [BioC] DESeq2 - input data questions
Michael Love
- [BioC] Defining the model matrix for a multi-factorial design with interactions - edgeR
Ryan
- [BioC] limma and Volcano Plots
Saket Choudhary
- [BioC] Multifactorial edgeR GLM design question (contrast that I should make)
James W. MacDonald
- [BioC] Unit tests with DNAString objects
Jonathon Hill [guest]
- [BioC] Pathview with minor species
Luo Weijun
- [BioC] restoring lattice-like format in flowViz?
D Ornelles
- [BioC] Unit tests with DNAString objects
Hervé Pagès
- [BioC] DESeq2 - input data questions
Ming Yi
- [BioC] questions on edgeR package
Ming Yi
- [BioC] Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Dale Watkins
- [BioC] FlowCore: problem with reading and writing fcs files
Mike
- [BioC] limma and Volcano Plots
Gordon K Smyth
- [BioC] EdgeR multi-factors testing questions
Gordon K Smyth
- [BioC] edgeR
Gordon K Smyth
- [BioC] questions on edgeR package
Gordon K Smyth
- [BioC] questions on edgeR package
Steve Lianoglou
- [BioC] limma-voom
Gordon K Smyth
- [BioC] Problem when trying to use \'affy\' package
Kaj
- [BioC] ggplot2 error
Alyaa Mahmoud
- [BioC] limma-voom
Ming Yi
- [BioC] edgeR
Jahn Davik
- [BioC] edgeR
Jahn Davik
- [BioC] questions on edgeR package
Gordon K Smyth
- [BioC] Best way of presenting a sub-fraction of edgeR RNAseq gene expression results in a publication
Sindre [guest]
- [BioC] Error during installation packages
Elodie Chapeaublanc
- [BioC] Defining the model matrix for a multi-factorial design with interactions - edgeR
Marco Pegoraro
- [BioC] questions on edgeR package
Steve Lianoglou
- [BioC] Gviz pacakge
Hahne, Florian
- [BioC] Problem when trying to use \'affy\' package
James W. MacDonald
- [BioC] Error during installation packages
James W. MacDonald
- [BioC] questions on edgeR package
Ming Yi
- [BioC] RMA normalization in large number of chips
Guilherme Rocha
- [BioC] RMA normalization in large number of chips
James W. MacDonald
- [BioC] (EdgeR) statistical justification of partitioning dataset for multiple analysis
Adriaan Sticker
- [BioC] EdgeR GOF plots
Adriaan Sticker
- [BioC] EdgeR: artifacts on BCV plot
Adriaan Sticker
- [BioC] (EdgeR) statistical justification of partitioning dataset for multiple analysis
Ryan
- [BioC] EdgeR: artifacts on BCV plot
Ryan
- [BioC] Using GOstats with ScanArray Express Data
Joseph Shaw [guest]
- [BioC] Using GOstats with ScanArray Express Data
Steve Lianoglou
- [BioC] EdgeR plotSmear varied size fo de.tag points
Gordon K Smyth
- [BioC] EdgeR plotSmear varied size fo de.tag points
Gordon K Smyth
- [BioC] Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Kasper Daniel Hansen
- [BioC] Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Dale Watkins
- [BioC] EdgeR: artifacts on BCV plot
Adriaan Sticker
- [BioC] EdgeR LogCpm and LogFC values calculation
Koen Van den Berge
- [BioC] EdgeR LogCpm and LogFC values calculation
P.D. Moerland
- [BioC] edgeR: fold change reported by exactTest for zero values of rna-seq
Nick N
- [BioC] (EdgeR) statistical justification of partitioning dataset for multiple analysis
Adriaan Sticker
- [BioC] summarizeOverlaps colData does NOT contain countBam() summary data
Cook, Malcolm
- [BioC] (EdgeR) statistical justification of partitioning dataset for multiple analysis
Ryan
- [BioC] Ontology
Orçun Haçarız [guest]
- [BioC] Ontology
Steve Lianoglou
- [BioC] Ontology
Steve Lianoglou
- [BioC] EdgeR LogCpm and LogFC values calculation
Koen Van den Berge
- [BioC] Ontology
Orcun Hacariz
- [BioC] Ontology
Steve Lianoglou
- [BioC] Ontology
Orcun Hacariz
- [BioC] Identifying genes that contribute to limma's roast/romer gene set enrichments
Stephen Hoang
- [BioC] minfi release 1.8
C T
Last message date:
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Archived on: Sat Feb 1 09:08:15 CET 2014
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