August 2012 Archives by thread

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Starting: Wed Aug 1 01:41:20 CEST 2012
Ending: Fri Aug 31 22:39:13 CEST 2012
Messages: 559

• [BioC] Error : package slot missing from signature for generic   Mark Cowley
  • [BioC] Error : package slot missing from signature for generic   Mark Cowley
    • [BioC] Error : package slot missing from signature for generic   Martin Morgan
      • [BioC] Error : package slot missing from signature for generic   Martin Morgan
      • [BioC] Error : package slot missing from signature for generic   Mark Cowley
• [BioC] read.maimages   Gordon K Smyth
  • [BioC] read.maimages   Assa Yeroslaviz
    • [BioC] read.maimages   Gordon K Smyth
• [BioC] edgeR, error in estimateCommonDisp   Gordon K Smyth
• [BioC] edgeR- data for case studies   Gordon K Smyth
  • [BioC] edgeR- data for case studies   Johnson, Franklin Theodore
• [BioC] general question about omogeneity of variances between microarray groups   Gordon K Smyth
• [BioC] Post-Doc - Milan: miRNAs and non-coding RNAs identification from RNAseq data   mattia pelizzola
• [BioC] DiffBind error loading dba.count   Paolo Kunderfranco
  • [BioC] DiffBind error loading dba.count   Gordon Brown
• [BioC] DESeq normalization   sudeep s
  • [BioC] DESeq normalization   Simon Anders
    • [BioC] DESeq normalization   sudeep s
      • [BioC] DESeq normalization   Simon Anders
      • [BioC] DESeq normalization   sudeep s
• [BioC] summarizeOverlaps - circular MT   Stefanie Tauber
  • [BioC] summarizeOverlaps - circular MT   Stefanie Tauber
  • [BioC] summarizeOverlaps - circular MT   Valerie Obenchain
• [BioC] multicore and DEXSeq   Alejandro Reyes
  • [BioC] multicore and DEXSeq   Lynn Amon
• [BioC] Variance stabilization of m-values   Gustavo Fernández Bayón
  • [BioC] Variance stabilization of m-values   Gordon K Smyth
    • [BioC] Variance stabilization of m-values   Tim Triche, Jr.
      • [BioC] Variance stabilization of m-values   Tim Triche, Jr.
      • [BioC] Variance stabilization of m-values   Gustavo Fernández Bayón
    • [BioC] Variance stabilization of m-values   Wolfgang Huber
      • [BioC] Variance stabilization of m-values   Gustavo Fernández Bayón
    • [BioC] Variance stabilization of m-values   Gustavo Fernández Bayón
    • [BioC] Variance stabilization of m-values   Brent Pedersen
      • [BioC] Variance stabilization of m-values   Gordon K Smyth
• [BioC] limma spottype   Assa Yeroslaviz
  • [BioC] limma spottype   James W. MacDonald
  • [BioC] assign vectors to many objects   John linux-user
• [BioC] more question about makeVennDiagram   Zhu, Lihua (Julie)
  • [BioC] more question about makeVennDiagram   Holly
    • [BioC] more question about makeVennDiagram   Zhu, Lihua (Julie)
  • [BioC] more question about makeVennDiagram   Zhu, Lihua (Julie)
    • [BioC] more question about makeVennDiagram   Holly
• [BioC] EdgeR and libsize normalization   Mark Robinson
• [BioC] Questions regarding MCRestimate package   Stella S [guest]
• [BioC] Package announcement: bsseq   Kasper Daniel Hansen
• [BioC] Seperate quantile normalization but common probe summary by median polish (oligo package)?   Johanna Schott [guest]
  • [BioC] Seperate quantile normalization but common probe summary by median polish (oligo package)?   Schott, Johanna
  • [BioC] Seperate quantile normalization but common probe summary by median polish (oligo package)?   James W. MacDonald
• [BioC] biomaRt 'Please report this to the mailing list'   John Coulthard
  • [BioC] biomaRt 'Please report this to the mailing list'   Sean Davis
• [BioC] Limma, arrayWeights and fold change   Amos Kirilovsky
  • [BioC] Limma, arrayWeights and fold change   Matthew Ritchie
    • [BioC] Limma, arrayWeights and fold change   Amos Kirilovsky
• [BioC] PhD student need advice   Al-Mamovy, Huda
  • [BioC] PhD student need advice   Steve Lianoglou
• [BioC] lumi - limma - geneSymbol and geneName N/A   Paolo Kunderfranco
• [BioC] oligo and pd.aragene.1.1.st annotation   Stephen Rolfe
  • [BioC] oligo and pd.aragene.1.1.st annotation   Marc Carlson
    • [BioC] oligo and pd.aragene.1.1.st annotation   Benilton Carvalho
      • [BioC] oligo and pd.aragene.1.1.st annotation   Stephen Rolfe
• [BioC] limma - NA values after withinarray normalization   Zhang, Xueqiong
  • [BioC] limma - NA values after withinarray normalization   Gordon K Smyth
• [BioC] edgeR exactTest dispersion value of 0 gives error   Surjyendu Ray [guest]
  • [BioC] edgeR exactTest dispersion value of 0 gives error   Gordon K Smyth
    • [BioC] edgeR exactTest dispersion value of 0 gives error   Gordon K Smyth
      • [BioC] edgeR exactTest dispersion value of 0 gives error   Gordon K Smyth
• [BioC] creating transcriptDB from gff3 files   gowtham
  • [BioC] creating transcriptDB from gff3 files   Valerie Obenchain
• [BioC] package xps   Steven
  • [BioC] package xps   Dan Tenenbaum
    • [BioC] package xps   Steven
      • [BioC] package xps   Steven
      • [BioC] package xps   cstrato
      • [BioC] package xps   Steven
      • [BioC] package xps   Dan Tenenbaum
      • [BioC] package xps   Steven
      • [BioC] package xps   cstrato
      • [BioC] package xps   Steven
      • [BioC] package xps   cstrato
• [BioC] Paired limma analysis   mb3058 at columbia.edu
  • [BioC] Paired limma analysis   James W. MacDonald
    • [BioC] Paired limma analysis   James W. MacDonald
• [BioC] limma: coefficient not estimable when dataset reduced by a few samples   Natasha Sahgal
  • [BioC] limma: coefficient not estimable when dataset reduced by a few samples   James W. MacDonald
  • [BioC] limma: coefficient not estimable when dataset reduced by a few samples   Gordon K Smyth
    • [BioC] limma: coefficient not estimable when dataset reduced by a few samples   Natasha Sahgal
• [BioC] computing segment areas on an image after thresholding   Ravi [guest]
  • [BioC] computing segment areas on an image after thresholding   Henrik Failmezger
    • [BioC] computing segment areas on an image after thresholding   ravi
      • [BioC] computing segment areas on an image after thresholding   Wolfgang Huber
• [BioC] easyRNASeq install problem   Loraine, Ann
  • [BioC] easyRNASeq install problem   Wolfgang Huber
  • [BioC] easyRNASeq install problem   Sean Davis
• [BioC] Scripts for CHARM data analysis   xiaojin li
  • [BioC] Scripts for CHARM data analysis   Tim Triche, Jr.
• [BioC] Marco Blanchette thought you would be interested in this station   mab at stowers.org
• [BioC] PDict in GenomicRanges   Hervé Pagès
  • [BioC] PDict in GenomicRanges   Hervé Pagès
• [BioC] Split SFF File with Bioconductor Package   Heidi [guest]
• [BioC] edgeR: design matrix for different condition   KJ Lim
  • [BioC] edgeR: design matrix for different condition   Gordon K Smyth
    • [BioC] edgeR: design matrix for different condition   KJ Lim
      • [BioC] edgeR: design matrix for different condition   Gordon K Smyth
      • [BioC] edgeR: design matrix for different condition   KJ Lim
      • [BioC] edgeR: design matrix for different condition   KJ Lim
      • [BioC] edgeR: Likelihood ratio test error   Gordon K Smyth
      • [BioC] edgeR: Likelihood ratio test error   KJ Lim
• [BioC] help with biomaRt bioconductor - Filter upstream_flank NOT FOUND problem   Tom Hait
  • [BioC] help with biomaRt bioconductor - Filter upstream_flank NOT FOUND problem   Wolfgang Huber
    • [BioC] help with biomaRt bioconductor - Filter upstream_flank NOT FOUND problem   Wolfgang Huber
    • [BioC] help with biomaRt bioconductor - Filter upstream_flank NOT FOUND problem   Steffen Durinck
• [BioC] ChippeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChippeakAnno   Chuang Kee Ong
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
  • [BioC] ChIPpeakAnno   Zhu, Lihua (Julie)
• [BioC] Visualizing the region of classification uncertainty on thresholded images   Ravi [guest]
  • [BioC] Visualizing the region of classification uncertainty on thresholded images   Alex Gutteridge
    • [BioC] Visualizing the region of classification uncertainty on thresholded images   ravi
      • [BioC] Visualizing the region of classification uncertainty on thresholded images   Alex Gutteridge
      • [BioC] Visualizing the region of classification uncertainty on thresholded images   ravi
      • [BioC] Visualizing the region of classification uncertainty on thresholded images   ravi
• [BioC] package xps HG-U133-PLUS_probe.tab / .psi   steven wink
  • [BioC] package xps HG-U133-PLUS_probe.tab / .psi   James W. MacDonald
    • [BioC] package xps HG-U133-PLUS_probe.tab / .psi   steven wink
• [BioC] Problem with nearest() in GenomicRanges   Chris Whelan
• [BioC] Back-estimating batch variables from SVA for ComBat?   Hollis Wright
  • [BioC] Back-estimating batch variables from SVA for ComBat?   Andrew Jaffe
    • [BioC] Back-estimating batch variables from SVA for ComBat?   Hollis Wright
• [BioC] error in exomeCopy - IRanges?   Lescai, Francesco
  • [BioC] error in exomeCopy - IRanges?   Mike Love
    • [BioC] error in exomeCopy - IRanges?   Lescai, Francesco
      • [BioC] error in exomeCopy - IRanges?   Michael Love
      • [BioC] error in exomeCopy - IRanges?   Lescai, Francesco
• [BioC] Bioinformatics Scientist opening in a startup on human genome interpretaion   Rong Chen
• [BioC] Linearity of "Scale rank invariant set" and "geometric mean" of normalizeCtData {HTqPCR}   Cytochalasin
• [BioC] DiffBind - overlap between different peak callers   Paolo Kunderfranco
  • [BioC] DiffBind - overlap between different peak callers   Paolo Kunderfranco
    • [BioC] DiffBind - overlap between different peak callers   Paolo Kunderfranco
      • [BioC] DiffBind - overlap between different peak callers   Gordon Brown
      • [BioC] DiffBind - overlap between different peak callers   Paolo Kunderfranco
• [BioC] cummeRbund issues   irene [guest]
  • [BioC] cummeRbund issues   Loyal A. Goff
• [BioC] edgeR: Likelihood ratio test error   KJ Lim
• [BioC] Question about ChIPpeakAnno R package   Zhu, Lihua (Julie)
  • [BioC] Question about ChIPpeakAnno R package: peakNearBDP   Zhu, Lihua (Julie)
• [BioC] annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)   Hari Easwaran
  • [BioC] annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)   James W. MacDonald
    • [BioC] annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)   Hari Easwaran
      • [BioC] annotation package for Agilent Human GE 4x44K v2 (catalog # G4845A)   Marc Carlson
• [BioC] deseq within and between group variation   sudeep s
  • [BioC] deseq within and between group variation   Simon Anders
    • [BioC] deseq within and between group variation   sudeep s
• [BioC] Granges for chromosome interactions   Bogdan Tanasa
  • [BioC] Granges for chromosome interactions   Tim Triche, Jr.
• [BioC] visualization of interactions   Bogdan Tanasa [guest]
  • [BioC] visualization of interactions   Tengfei Yin
• [BioC] error in DEXSeq fitDispersionFunction()   Alejandro Reyes
  • [BioC] error in DEXSeq fitDispersionFunction()   Georg Otto
    • [BioC] error in DEXSeq fitDispersionFunction()   Alejandro Reyes
      • [BioC] error in DEXSeq fitDispersionFunction()   Wolfgang Huber
      • [BioC] error in DEXSeq fitDispersionFunction()   Martin Morgan
• [BioC] ChIPpeakAnno to find peaks nearest to miRNA   Zhu, Lihua (Julie)
• [BioC] HT qPCR; Creating qPCRset from expression matrix   Cytochalasin
  • [BioC] HT qPCR; Creating qPCRset from expression matrix   Heidi Dvinge
• [BioC] ontoCompare   Oana VIGY
  • [BioC] ontoCompare   Brad Davis
    • [BioC] ontoCompare   Oana VIGY
• [BioC] ChipPeakAnno: 4-way venn diagram   José LÓPEZ
  • [BioC] ChipPeakAnno: 4-way venn diagram   Zhu, Lihua (Julie)
    • [BioC] ChipPeakAnno: 4-way venn diagram   José LÓPEZ
    • [BioC] ChipPeakAnno: 4-way venn diagram   Wolfgang Huber
      • [BioC] ChipPeakAnno: 4-way venn diagram   Zhu, Lihua (Julie)
      • [BioC] ChipPeakAnno: 4-way venn diagram   Heidi Dvinge
      • [BioC] FW: ChipPeakAnno: 4-way venn diagram   Zhu, Lihua (Julie)
      • [BioC] FW: ChipPeakAnno: 4-way venn diagram   Wolfgang Huber
      • [BioC] ChipPeakAnno: 4-way venn diagram   Zhu, Lihua (Julie)
      • [BioC] ChipPeakAnno: 4-way venn diagram   Steffen Möller
• [BioC] help - HTqPCR and lightcycler   Heidi Dvinge
• [BioC] bioconductor implementations to find rank invariant genes   Juliet Hannah
  • [BioC] bioconductor implementations to find rank invariant genes   Heidi Dvinge
• [BioC] About ensembl genes   chris Jhon
  • [BioC] About ensembl genes   Paul Leo
    • [BioC] About ensembl genes   chris Jhon
      • [BioC] About ensembl genes   Paul Leo
      • [BioC] About ensembl genes   chris Jhon
• [BioC] rtracklayer blocks function   Janet Young
  • [BioC] rtracklayer blocks function   Michael Lawrence
    • [BioC] rtracklayer blocks function   Janet Young
      • [BioC] rtracklayer blocks function   Michael Lawrence
• [BioC] Openening qPCR file from ABI   Philippe [guest]
  • [BioC] Openening qPCR file from ABI   Prof. Dr. Matthias Kohl
  • [BioC] Openening qPCR file from ABI   Hooiveld, Guido
    • [BioC] Openening qPCR file from ABI   Heidi Dvinge
• [BioC] edgeR---question   Asma rabe
  • [BioC] edgeR---question   Gordon K Smyth
• [BioC] minfi not available for R vs 2.15.1   chris briggs [guest]
  • [BioC] minfi not available for R vs 2.15.1   Dan Tenenbaum
    • [BioC] minfi not available for R vs 2.15.1   Dan Tenenbaum
• [BioC] Confirming a batch effect has been removed   Hoyles, Lesley
  • [BioC] Confirming a batch effect has been removed   James W. MacDonald
    • [BioC] Confirming a batch effect has been removed   Hoyles, Lesley
• [BioC] cosmo vignette example error   Simon [guest]
• [BioC] how to get a gene list for profilePlots in Repitools package   rong [guest]
  • [BioC] how to get a gene list for profilePlots in Repitools package   Dario Strbenac
• [BioC] (no subject)   Gordon K Smyth
• [BioC] total gene number for a given species in reactome.db   Gang Feng
  • [BioC] total gene number for a given species in reactome.db   Marc Carlson
• [BioC] edgeR: Value of variation of biological variation (BCV)   KJ Lim
  • [BioC] edgeR: Value of variation of biological variation (BCV)   Gordon K Smyth
    • [BioC] edgeR: Value of variation of biological variation (BCV)   KJ Lim
    • [BioC] edgeR: Value of variation of biological variation (BCV)   Lucia Peixoto
      • [BioC] edgeR: Value of variation of biological variation (BCV)   Gordon K Smyth
• [BioC] overlap GRangesList and vcf   Georg Otto
  • [BioC] overlap GRangesList and vcf   Valerie Obenchain
• [BioC] on PWM in biostrings   Hervé Pagès
  • [BioC] on PWM in biostrings   Eloi Mercier
    • [BioC] on PWM in biostrings   Shouyong Peng
• [BioC] Job openings: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital   Wittner, Ben, Ph.D.
• [BioC] A doubt with contrasts in limma   Cittaro Davide
  • [BioC] A doubt with contrasts in limma   James W. MacDonald
    • [BioC] A doubt with contrasts in limma   Cittaro Davide
• [BioC] using RUnit inspect() feature in package testing   Levi Waldron
  • [BioC] using RUnit inspect() feature in package testing   Dan Tenenbaum
  • [BioC] using RUnit inspect() feature in package testing   Paul Shannon
• [BioC] Should AgiMicroRna and GeneSpring quantile normalisation be the same ?   Seyit Ali KAYIS
  • [BioC] Should AgiMicroRna and GeneSpring quantile normalisation be the same ?   Paul Geeleher
    • [BioC] Should AgiMicroRna and GeneSpring quantile normalisation's results be the same ?   Seyit Ali KAYIS
    • [BioC] Should AgiMicroRna and GeneSpring quantile normalisation's results be the same ?   Seyit Ali KAYIS
      • [BioC] Should AgiMicroRna and GeneSpring quantile normalisation's results be the same ?   Martin Morgan
• [BioC] Lumi loading problem   Pan Du
• [BioC] how to set parameter of DESeq function estimateDispersions   wang peter
• [BioC] Problem with Graphvix   Con Menictas [guest]
  • [BioC] Problem with Graphvix   Sean Davis
• [BioC] edgeR: DE summary of decideTestsDGE   KJ Lim
  • [BioC] edgeR: DE summary of decideTestsDGE   Yunshun Chen
    • [BioC] edgeR: DE summary of decideTestsDGE   KJ Lim
• [BioC] DEXSeq: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE   sheng zhao
  • [BioC] DEXSeq: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE   Alejandro Reyes
• [BioC] mcmapply with edgeR?   Aaron Mackey
  • [BioC] mcmapply with edgeR?   Martin Morgan
    • [BioC] mcmapply with edgeR?   Aaron Mackey
• [BioC] affy: batch completely confounded with treatment   Juliet Hannah
  • [BioC] affy: batch completely confounded with treatment   Matthew McCall
  • [BioC] affy: batch completely confounded with treatment   W. Evan Johnson
    • [BioC] Failed loading Biobase   joseph
      • [BioC] Failed loading Biobase   Sean Davis
      • [BioC] Failed loading Biobase   Dan Tenenbaum
• [BioC] Fwd: help   rakesh sharma
  • [BioC] Fwd: help   Heidi Dvinge
    • [BioC] Fwd: help   Heidi Dvinge
• [BioC] help   rakesh sharma [guest]
• [BioC] HtqPCR-help   rakesh sharma
• [BioC] how to plot quality report   wang peter
  • [BioC] how to plot quality report   Martin Morgan
• [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH   Gabriel Wajnberg [guest]
  • [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH   Benilton Carvalho
    • [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH   Gabriel Wajnberg
      • [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH   Benilton Carvalho
      • [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH   Gabriel Wajnberg
• [BioC] [Limma] Can I adjust family relationship in Limma?   Yao Chen
• [BioC] RankProd package paired-sample sesign   Maider Muñoz
• [BioC] extracting specific columns in R   Fatemehsadat Seyednasrollah
  • [BioC] extracting specific columns in R   Sean Davis
  • [BioC] Gene enrichment question   Aliaksei Holik
    • [BioC] Gene enrichment question   Steve Lianoglou
    • [BioC] Gene enrichment question   Alex Gutteridge
    • [BioC] Gene enrichment question   Michael Salbaum
      • [BioC] Gene enrichment question   Aliaksei Holik
      • [BioC] Gene enrichment question   Alex Gutteridge
    • [BioC] Gene enrichment question   Wu, Di
• [BioC] cummerbund   i b
• [BioC] Affymetrix annotation using R or NetAffx   Natasha Sahgal
  • [BioC] Affymetrix annotation using R or NetAffx   James W. MacDonald
    • [BioC] Affymetrix annotation using R or NetAffx   James W. MacDonald
      • [BioC] Affymetrix annotation using R or NetAffx   Natasha Sahgal
• [BioC] design question   farnoosh sheikhi
  • [BioC] design question   Gordon K Smyth
• [BioC] useDevel and update all packages - wrong library location?   Janet Young
  • [BioC] useDevel and update all packages - wrong library location?   Martin Morgan
• [BioC] Can I adjust family relationship in Limma?   Gordon K Smyth
• [BioC] RankProd paired-sample analysis   Maider Muñoz Culla
• [BioC] How to convert multipe tables into one table in a dataframe   taj [guest]
  • [BioC] How to convert multipe tables into one table in a dataframe   Dan Tenenbaum
• [BioC] Regarding an issue with easyRNASeq - from Surjyendu Ray.   Nicolas Delhomme
  • [BioC] Regarding an issue with easyRNASeq - from Surjyendu Ray.   Nicolas Delhomme
• [BioC] package xps: export.filter issues   steven wink
  • [BioC] package xps: export.filter issues   cstrato
  • [BioC] package xps: export.filter issues   cstrato
  • [BioC] package xps: export.filter issues   cstrato
• [BioC] Affymetrix gene st array - ok to do statistics on Category:Main only?   Martin O'Hare
• [BioC] 4 Positions at EMBL   Wolfgang Huber
• [BioC] OTU delimitation from simple fasta (sanger) sequences   Martin Unterseher
• [BioC] Marray Quality Check   Tim Cam [guest]
  • [BioC] Marray Quality Check   Jean Yang
    • [BioC] Marray Quality Check   Tim Cam
• [BioC] Where to get BAM files for easyRNASeq human use case   Richard Friedman
  • [BioC] Where to get BAM files for easyRNASeq human use case   Nicolas Delhomme
    • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Richard Friedman
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Steve Lianoglou
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Richard Friedman
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Martin Morgan
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Richard Friedman
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Nicolas Delhomme
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Nicolas Delhomme
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Wolfgang Huber
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Steve Lianoglou
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Martin Morgan
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Wolfgang Huber
      • [BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION   Nicolas Delhomme
• [BioC] good news and bad news   Hervé Pagès
  • [BioC] good news and bad news   Michael Lawrence
    • [BioC] good news and bad news   Steve Lianoglou
    • [BioC] good news and bad news   Hervé Pagès
      • [BioC] good news and bad news   Tim Triche, Jr.
      • [BioC] good news and bad news   Kasper Daniel Hansen
      • [BioC] Good practice for choosing biological groups to include in array analysis   Salvador
      • [BioC] Good practice for choosing biological groups to include in array analysis   Sean Davis
  • [BioC] good news and bad news   Steve Lianoglou
• [BioC] question for limma   Jia, Hui
  • [BioC] question for limma   Gordon K Smyth
• [BioC] In silico protein digestion   David Gibbs
• [BioC] Question about interpretation of CHARM results   zeynep özkeserli
  • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
    • [BioC] Question about interpretation of CHARM results   zeynep özkeserli
      • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
      • [BioC] Question about interpretation of CHARM results   zeynep özkeserli
      • [BioC] Question about interpretation of CHARM results   Brian Herb
      • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
      • [BioC] Question about interpretation of CHARM results   Kevin R. Coombes
      • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
      • [BioC] Question about interpretation of CHARM results   Brent Pedersen
      • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
      • [BioC] Question about interpretation of CHARM results   Brent Pedersen
      • [BioC] Question about interpretation of CHARM results   Tim Triche, Jr.
  • [BioC] Question about interpretation of CHARM results   Andrew Jaffe
  • [BioC] Question about interpretation of CHARM results   Andrew Jaffe
• [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Olin Silander
  • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Dan Tenenbaum
    • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Dan Tenenbaum
      • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Dan Tenenbaum
      • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Olin Silander
      • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Olin Silander
      • [BioC] Problems installing EBImage - Symbol not found: _gdk_display   Dan Tenenbaum
• [BioC] GPL2893 and GPL875 probe Sequnces   Reema Singh
  • [BioC] GPL2893 and GPL875 probe Sequnces   Sean Davis
    • [BioC] GPL2893 and GPL875 probe Sequnces   Sean Davis
• [BioC] Problem with addGeneIDs and org.Sc.sgd.db   Susan Wilson
  • [BioC] Problem with addGeneIDs and org.Sc.sgd.db   Marc Carlson
• [BioC] Test   cstrato
  • [BioC] Test   cstrato
• [BioC] affy hugene 2.1 st   Dario Greco
  • [BioC] affy hugene 2.1 st   James W. MacDonald
  • [BioC] affy hugene 2.1 st   Christian Stratowa [guest]
• [BioC] GRanges DitancetoNearest query   d r
  • [BioC] GRanges DitancetoNearest query   Steve Lianoglou
    • [BioC] GRanges DitancetoNearest query   d r
      • [BioC] GRanges DitancetoNearest query   Sean Davis
      • [BioC] GRanges DitancetoNearest query   d r
• [BioC] distanceToNearest for GRanges?   Janet Young
  • [BioC] distanceToNearest for GRanges?   Valerie Obenchain
    • [BioC] distanceToNearest for GRanges?   Valerie Obenchain
• [BioC] nearest for GRanges ignoring overlapping ranges   Janet Young
  • [BioC] nearest for GRanges ignoring overlapping ranges   Valerie Obenchain
• [BioC] limma   Novak Jaroslav
  • [BioC] limma   Sean Davis
    • [BioC] limma   Sean Davis
• [BioC] load local genbank file   Hu, Bin
  • [BioC] load local genbank file   Vincent Carey
    • [BioC] load local genbank file   Vincent Carey
      • [BioC] load local genbank file   Hu, Bin
• [BioC] Parsing values from DGEExact$table (created via edgeR)   KJ Lim
  • [BioC] Parsing values from DGEExact$table (created via edgeR)   James W. MacDonald
• [BioC] KEGGSOAP: list.pathways(org) or alternative way   Jenny Kartsaki
  • [BioC] KEGGSOAP: list.pathways(org) or alternative way   Marc Carlson
    • [BioC] KEGGSOAP: list.pathways(org) or alternative way   Marc Carlson
• [BioC] RNA-seq data simulation   Alpesh Querer
  • [BioC] RNA-seq data simulation   Alpesh Querer
    • [BioC] RNA-seq data simulation   Mark Robinson
      • [BioC] RNA-seq data simulation   Aaron Mackey
      • [BioC] RNA-seq data simulation   Marcus Davy
• [BioC] distance to TSS upstream/downstream   d r
  • [BioC] distance to TSS upstream/downstream   Michael Lawrence
    • [BioC] distance to TSS upstream/downstream   d r
• [BioC] GenomicRanges: nearest() for GRanges not returning overlaps   Valerie Obenchain
• [BioC] GViz: Ucsctrack Issue   Winston Timp
  • [BioC] GViz: UcscTrack Issue   Winston Timp
    • [BioC] GViz: UcscTrack Issue   Vincent Carey
      • [BioC] GViz: UcscTrack Issue   Winston Timp
• [BioC] GOSemSim mgeneSim GO.BP calculation time   Sandeep Amberkar [guest]
• [BioC] Encrypting IDAT files using IDATreader   Yoo, Seungyeul
  • [BioC] Encrypting IDAT files using IDATreader   Mike Smith
    • [BioC] Encrypting IDAT files using IDATreader   Yoo, Seungyeul
      • [BioC] Encrypting IDAT files using IDATreader   Mike Smith
      • [BioC] Encrypting IDAT files using IDATreader   Yoo, Seungyeul
    • [BioC] Encrypting IDAT files using IDATreader   Kasper Daniel Hansen
      • [BioC] Encrypting IDAT files using IDATreader   Mark Cowley
      • [BioC] Encrypting IDAT files using IDATreader   Yoo, Seungyeul
      • [BioC] Encrypting IDAT files using IDATreader   Tim Triche, Jr.
      • [BioC] Encrypting IDAT files using IDATreader   Henrik Bengtsson
• [BioC] #Identify differentially expressed genes   Paolo Kunderfranco
  • [BioC] #Identify differentially expressed genes   Pan Du
    • [BioC] #Identify differentially expressed genes   Paolo Kunderfranco
      • [BioC] #Identify differentially expressed genes   Pan Du
  • [BioC] #Identify differentially expressed genes   Gordon K Smyth
• [BioC] how to check the parameters of the function ShortRead:::.freqSequences?   wang peter
  • [BioC] how to check the parameters of the function ShortRead:::.freqSequences?   Steve Lianoglou
    • [BioC] how to check the parameters of the function ShortRead:::.freqSequences?   Steve Lianoglou
  • [BioC] how to check the parameters of the function ShortRead:::.freqSequences?   Martin Morgan
• [BioC] Gviz: plotTracks with GeneRegionTrack   Winston Timp
  • [BioC] Gviz: plotTracks with GeneRegionTrack   Hahne, Florian
• [BioC] RNA-seq analysis and two-way ANOVAs   Elena Sorokin
  • [BioC] RNA-seq analysis and two-way ANOVAs   Gordon K Smyth
• [BioC] readPositonalinfo   adesh ashok
  • [BioC] readPositonalinfo   Dario Strbenac
• [BioC] Job: Research Associate in Bioinformatics, Cambridge, UK   Krys Kelly
• [BioC] Subsetting "sites only" VCF objects   Richard Pearson
  • [BioC] Subsetting "sites only" VCF objects   Valerie Obenchain
• [BioC] readPositionalInfo   adesh ashok
  • [BioC] readPositionalInfo   Sean Davis
• [BioC] shortread base quality   David martin
  • [BioC] shortread base quality   Martin Morgan
    • [BioC] shortread base quality   David martin
      • [BioC] shortread base quality   Martin Morgan
      • [BioC] shortread base quality   David martin
      • [BioC] shortread base quality   Martin Morgan
      • [BioC] shortread base quality   David Vilanova
      • [BioC] shortread base quality   Martin Morgan
• [BioC] about the model.matrix function?   wang peter
• [BioC] how to make makeContrast in edgeR?   wang peter
  • [BioC] how to make makeContrast in edgeR?   KJ Lim
    • [BioC] how to make makeContrast in edgeR?   wang peter
  • [BioC] how to make makeContrast in edgeR?   Sean Davis
    • [BioC] how to make makeContrast in edgeR?   wang peter
      • [BioC] how to make makeContrast in edgeR?   wang peter
      • [BioC] how to make makeContrast in edgeR?   Sean Davis
      • [BioC] how to make makeContrast in edgeR?   wang peter
      • [BioC] how to make makeContrast in edgeR?   KJ Lim
      • [BioC] how to make makeContrast in edgeR?   wang peter
      • [BioC] how to make makeContrast in edgeR?   wang peter
      • [BioC] how to make makeContrast in edgeR?   KJ Lim
• [BioC] report a potential bug in edgeR   wang peter
  • [BioC] report a potential bug in edgeR   Gordon K Smyth
• [BioC] Plausibilty of application of "modified LOESS normalization" to single channel arrays   Cytochalasin
  • [BioC] Plausibilty of application of "modified LOESS normalization" to single channel arrays   Cytochalasin
• [BioC] Installation of Annmap   Jeremy Ng
  • [BioC] Installation of Annmap   Sean Davis
    • [BioC] Installation of Annmap   Nathan Salomonis
• [BioC] DESeq Fold-Change calculation   Lana Schaffer
  • [BioC] DESeq Fold-Change calculation   Simon Anders
    • [BioC] DESeq Fold-Change calculation   Lana Schaffer
• [BioC] DESeq variance stabilization   Lana Schaffer
  • [BioC] DESeq variance stabilization   Steve Lianoglou
    • [BioC] DESeq variance stabilization   Lana Schaffer
      • [BioC] DESeq variance stabilization   Steve Lianoglou
• [BioC] HTqPCR problems   cfischer
• [BioC] Beadarray Filtering by Probequality   Will [guest]
• [BioC] Variability in microarray data   Adrián [guest]
• [BioC] urgent help: meet an error in using edgeR   wang peter
  • [BioC] urgent help: meet an error in using edgeR   Martin Morgan
• [BioC] Fwd: ASSIST on contrast matrix   Seyed Ahmad Mousavi
• [BioC] plotMDS EdgeR/limma   Kaat De Cremer
  • [BioC] plotMDS EdgeR/limma   Gordon K Smyth
• [BioC] lumi - Heatmap   Paolo Kunderfranco
  • [BioC] lumi - Heatmap   Sean Davis
• [BioC] Rgraphviz- \"len\" is not a graphical parameter   narsis [guest]
  • [BioC] Rgraphviz- \"len\" is not a graphical parameter   Kasper Daniel Hansen
    • [BioC] Rgraphviz- \"len\" is not a graphical parameter   Martin Morgan
    • [BioC] Rgraphviz- \"len\" is not a graphical parameter   Narsis Kiani
• [BioC] strange results with edgeR::goodTuring   Francois Pepin
  • [BioC] strange results with edgeR::goodTuring   Gordon K Smyth
    • [BioC] strange results with edgeR::goodTuring   Francois Pepin
• [BioC] package xps and affy hugene 2.1 st   cstrato
• [BioC] EBImage and redhat   Brian Pettegrew
• [BioC] RE ChIPPEAKANNO   Zhu, Lihua (Julie)
  • [BioC] RE ChIPPEAKANNO   Ngeow, Joanne
  • [BioC] RE ChIPPEAKANNO   Zhu, Lihua (Julie)
  • [BioC] RE ChIPPEAKANNO   Zhu, Lihua (Julie)
• [BioC] Paired two-color design   January Weiner
  • [BioC] Paired two-color design   Gordon K Smyth
    • [BioC] Paired two-color design   January Weiner
    • [BioC] Paired two-color design   Gordon K Smyth
      • [BioC] Paired two-color design   January Weiner
      • [BioC] Paired two-color design   Gordon K Smyth
• [BioC] Differential expression without replicates   Srinivas M. Srikanth
  • [BioC] Differential expression without replicates   Mark Robinson
    • [BioC] Differential expression without replicates   Wolfgang Huber
      • [BioC] Differential expression without replicates   Srinivas M. Srikanth
• [BioC] segmentation fault in rma.background.correct()   Axel Klenk
• [BioC] design and contrat matrix in limma for Affymetrix arrays   Jorge Miró
  • [BioC] design and contrat matrix in limma for Affymetrix arrays   James W. MacDonald
    • [BioC] design and contrat matrix in limma for Affymetrix arrays   Jorge Miró
• [BioC] Understanding the columns in the limma results output   Jorge Miró
  • [BioC] Understanding the columns in the limma results output   James W. MacDonald
    • [BioC] Understanding the columns in the limma results output   Jorge Miró
      • [BioC] Understanding the columns in the limma results output   James W. MacDonald
      • [BioC] Understanding the columns in the limma results output   Jorge Miró
      • [BioC] Understanding the columns in the limma results output   James W. MacDonald
      • [BioC] Understanding the columns in the limma results output   Jorge Miró
      • [BioC] Understanding the columns in the limma results output   Jorge Miró
  • [BioC] Understanding the columns in the limma results output   Jorge Miró
• [BioC] question about edgeR smearPlot   Ann Loraine
• [BioC] intersecting GRanges with UCSCTableQuery   d r
  • [BioC] intersecting GRanges with UCSCTableQuery   Michael Lawrence
• [BioC] clustering genes in GO categories   Assa Yeroslaviz
  • [BioC] clustering genes in GO categories   Martin Morgan
• [BioC] regarding edgeR   deepika lakhwani
  • [BioC] regarding edgeR   Steve Lianoglou
• [BioC] How to combine VCF-class and data.frame with annotations   Stefan Dentro
  • [BioC] How to combine VCF-class and data.frame with annotations   Vincent Carey
    • [BioC] How to combine VCF-class and data.frame with annotations   Stefan Dentro
      • [BioC] How to combine VCF-class and data.frame with annotations   Martin Morgan
• [BioC] summarizeOverlaps question   James W. MacDonald
  • [BioC] summarizeOverlaps question   Valerie Obenchain
    • [BioC] summarizeOverlaps question   James W. MacDonald
      • [BioC] summarizeOverlaps question   Valerie Obenchain
• [BioC] biomart database version problem   lemon tree
  • [BioC] biomart database version problem   James W. MacDonald
  • [BioC] biomart database version problem   Steffen Durinck
    • [BioC] biomart database version problem   lemon tree
• [BioC] ChIPpeakAnno - c elegans annotation feature type: translation start site   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno - getAnnotation   Zhu, Lihua (Julie)
• [BioC] problem with accessing the files   Noushin Farnoud
  • [BioC] problem with accessing the files   Sean Davis
• [BioC] modules incompatible with R 2.15.1   Marcus Moeller
  • [BioC] modules incompatible with R 2.15.1   Sean Davis
    • [BioC] modules incompatible with R 2.15.1   Marcus Moeller
      • [BioC] modules incompatible with R 2.15.1   Sean Davis
• [BioC] elementary question about statistical comparing of standard deviations, pls help   Cytochalasin
• [BioC] ChipPeakAnno / GRanges isolate peaks that do NOT overlap   José LÓPEZ
  • [BioC] ChipPeakAnno / GRanges isolate peaks that do NOT overlap   Zhu, Lihua (Julie)
• [BioC] reviews for quality control   carol white
  • [BioC] reviews for quality control   Paul Geeleher
    • [BioC] reviews for quality control   carol white
• [BioC] find DE by edgeR   wang peter
• [BioC] How does limma t-test work?   Jorge Miró
  • [BioC] How does limma t-test work?   James W. MacDonald
• [BioC] How to use cutome reference genome?   Yan He [guest]
  • [BioC] How to use cutome reference genome?   Kasper Daniel Hansen
• [BioC] Data set for comparing statistical tests   Jorge Miró
  • [BioC] Data set for comparing statistical tests   Benilton Carvalho
    • [BioC] Data set for comparing statistical tests   Jorge Miró
    • [BioC] Data set for comparing statistical tests   Jorge Miró
      • [BioC] Data set for comparing statistical tests   James W. MacDonald
• [BioC] pdmClass plot error   Jonah Mushava
• [BioC] regarding mapping package   deepika lakhwani
• [BioC] Biostrings DNAMultipleAlignment vs AlignedXStringSet   Nathan Sheffield [guest]
  • [BioC] Biostrings DNAMultipleAlignment vs AlignedXStringSet   Martin Morgan
• [BioC] Difference in DABG between XPS package and APT   zaid haddad [guest]
  • [BioC] Difference in DABG between XPS package and APT   cstrato
• [BioC] Rgraphviz (news, testing)   Kasper Daniel Hansen
• [BioC] Problem while working with GOSim package   Anirban Bhar
• [BioC] BLAST - annotate package?   Tim Smith
  • [BioC] BLAST - annotate package?   James W. MacDonald
    • [BioC] BLAST - annotate package?   Tim Smith
      • [BioC] BLAST - annotate package?   James W. MacDonald

Last message date: Fri Aug 31 22:39:13 CEST 2012
Archived on: Sat Sep 1 08:05:33 CEST 2012

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