March 2012 Archives by author

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Starting: Thu Mar 1 00:46:17 CET 2012
Ending: Sat Mar 31 17:04:59 CEST 2012
Messages: 777

• [BioC] creating GRanges and reading BAM files   David A.
• [BioC] creating GRanges and reading BAM files   David A.
• [BioC] creating GRanges and reading BAM files   David A.
• [BioC] Is this a basic bug or something else ?   ALok
• [BioC] PostForm() with KEGG   Ovokeraye Achinike-Oduaran
• [BioC] Limma and negative p-values   Ovokeraye Achinike-Oduaran
• [BioC] Limma and negative p-values   Ovokeraye Achinike-Oduaran
• [BioC] Limma and negative p-values   Ovokeraye Achinike-Oduaran
• [BioC] Limma and negative p-values   Ovokeraye Achinike-Oduaran
• [BioC] getGEO and wilcox.test   Ovokeraye Achinike-Oduaran
• [BioC] getGEO and wilcox.test   Ovokeraye Achinike-Oduaran
• [BioC] getGEO and wilcox.test   Ovokeraye Achinike-Oduaran
• [BioC] Using the untar() with getGEOSuppFiles()   Ovokeraye Achinike-Oduaran
• [BioC] plotting a CA   Aedin
• [BioC] DESeq estimateDispersion options for lower depth miRNA-seq   Aggarwal, Praful
• [BioC] DESeq estimateDispersion options for lower depth   Aggarwal, Praful
• [BioC] DESeq estimateDispersion options for lower depth   Aggarwal, Praful
• [BioC] DESeq estimateDispersion options for lower depth miRNA-seq   Aggarwal, Praful
• [BioC] beadarray package: BASH error   Kemal Akat
• [BioC] problems generating a gene2GOlist in topGO   Adrian Alexa
• [BioC] World's biggest fake conference in computer science   James Allen
• [BioC] Chairman disappears from world's biggest computer conference   James Allen
• [BioC] error in using random forest   Naomi Altman
• [BioC] error in using random forest   Naomi Altman
• [BioC] fisher exact test pairwise comparisons   Naomi Altman
• [BioC] Limma and negative p-values   Naomi Altman
• [BioC] Help with plot comparison   Simon Anders
• [BioC] re incomplete analysis in Deseq   Simon Anders
• [BioC] A few Q's on using DEXSeq with mucho data   Simon Anders
• [BioC] A few Q's on using DEXSeq with mucho data   Simon Anders
• [BioC] edgeR i get 377 significant genes where in DESeq i got 0   Simon Anders
• [BioC] DESeq without replicates, Problem trying to obtain significant hits   Simon Anders
• [BioC] Limma and negative p-values   Simon Anders
• [BioC] DESeq Question   Simon Anders
• [BioC] DESeq multi-factor export results   Simon Anders
• [BioC] DESeq multi-factor export results   Simon Anders
• [BioC] DESeq vs DEXSeq   Simon Anders
• [BioC] Up & Downregulated genes using DESeq   Simon Anders
• [BioC] Up & Downregulated genes using DESeq   Simon Anders
• [BioC] Up & Downregulated genes using DESeq   Simon Anders
• [BioC] EBImage: Negative pixel intensities?!?   Henrik Bengtsson
• [BioC] EBImage: Negative pixel intensities?!?   Henrik Bengtsson
• [BioC] unable to readImage using EBImage package   Henrik Bengtsson
• [BioC] Help with plot comparison   Tina Asante Boahene
• [BioC] Help with plot comparison   Tina Asante Boahene
• [BioC] Plot Cumulative graph   Tina Asante Boahene
• [BioC] Copy number analysis   Fred Boehm
• [BioC] edgeR-How to obtain a list of normalized expression values   Philipp Brand
• [BioC] Help with plot comparison   Vince S. Buffalo
• [BioC] Newer version of DESeq give much small list of DE genes   Vince S. Buffalo
• [BioC] limma package topTable error   Vincent Carey
• [BioC] snpStats, read.long, alleles in two columns   Vincent Carey
• [BioC] snpStats, read.long, alleles in two columns   Vincent Carey
• [BioC] how can i apply random forest to expression sets of dna microarray   Vincent Carey
• [BioC] getGEO and wilcox.test   Vincent Carey
• [BioC] Please help: SNP Frequency Analysis Package in Bioconductor   Vincent Carey
• [BioC] saving GRangesList object; conversion to GFF   Vincent Carey
• [BioC] Using Anova for microarray data   Vincent Carey
• [BioC] GRENITS won't run with example data   Vincent Carey
• [BioC] dispatch method   Vincent Carey
• [BioC] Rsamtools installation   Vincent Carey
• [BioC] DNAcopy for CNV in SNP Affy 6.0   Vincent Carey
• [BioC] problem creating own org.Ss.eg.db   Marc Carlson
• [BioC] how to get gene list for given GO terms?   Marc Carlson
• [BioC] AnnotationDbi - makeOrgPackageFromNCBI - gene_info table is not populated   Marc Carlson
• [BioC] KEGGSOAP   Marc Carlson
• [BioC] How can I access to a gene set   Marc Carlson
• [BioC] how to make line graph   Benilton Carvalho
• [BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"   Benilton Carvalho
• [BioC] for running arrayQualityMetrics   Benilton Carvalho
• [BioC] pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays   Benilton Carvalho
• [BioC] crlmm and Affymetrix SNP5 array [genotyping issues]   Benilton Carvalho
• [BioC] GRENITS won't run with example data   Benilton Carvalho
• [BioC] pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays   Benilton Carvalho
• [BioC] oligo package: extracting position, sequence, and intensity from Affymetrix tiling array   Benilton Carvalho
• [BioC] oligo package: extracting position, sequence, and intensity from Affymetrix tiling array   Benilton Carvalho
• [BioC] how to rank affy probesets by their probe-effect magnitude   Robert Castelo
• [BioC] how to rank affy probesets by their probe-effect magnitude   Robert Castelo
• [BioC] how to rank affy probesets by their probe-effect magnitude   Robert Castelo
• [BioC] Copy number analysis   Mete Civelek
• [BioC] snpStats, read.long, alleles in two columns   David Clayton
• [BioC] Copy number analysis   Djork-Arné Clevert
• [BioC] breastCancerMAINZ package installation problem   Coghlan, Avril
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Cook, Malcolm
• [BioC] distanceToNearest for GRanges?   Cook, Malcolm
• [BioC] ChIPpeakAnno as.data.frame error   Mark Cowley
• [BioC] ChIPpeakAnno as.data.frame error   Mark Cowley
• [BioC] ChIPpeakAnno as.data.frame error   Mark Cowley
• [BioC] Copy Number Analysis for Mapreduce   My Coyne
• [BioC] Newer version of DESeq give much small list of DE genes   Creasy, Todd
• [BioC] Newer version of DESeq give much small list of DE genes   Creasy, Todd
• [BioC] Problems using arrayQualityMetrics   Rosalind Cutts
• [BioC] Problems using arrayQualityMetrics   Rosalind Cutts
• [BioC] DESeq Question   Omar Darwish
• [BioC] DESeq Question   Omar Darwish
• [BioC] Up & Downregulated genes using DESeq   Omar Darwish
• [BioC] Up & Downregulated genes using DESeq   Omar Darwish
• [BioC] Difficulty in AnnotatedDataFrame   Deepak Datta
• [BioC] Provide an Example for AnnotatedDataFrame   Deepak Datta
• [BioC] New to Bioconductor is there a better way?   Davis, Brian
• [BioC] How to include external applications in package vignette code?   Sean Davis
• [BioC] Gene-Metabolite correlation network   Sean Davis
• [BioC] Gene-Metabolite correlation network   Sean Davis
• [BioC] Genetic coding impact on variant calling   Sean Davis
• [BioC] Question about Normalization   Sean Davis
• [BioC] how to get pig genome and for miRNA target scan   Sean Davis
• [BioC] problems using the latest version of e1071 (svm)   Sean Davis
• [BioC] Ensembl and refseq genes   Sean Davis
• [BioC] an error from ShortRead   Sean Davis
• [BioC] how to map Affymetrix ID to ensemble gene ID   Sean Davis
• [BioC] biomaRt cannot find getAffyArrays function   Sean Davis
• [BioC] how to map Affymetrix ID to ensemble gene ID   Sean Davis
• [BioC] how to map Affymetrix ID to ensemble gene ID   Sean Davis
• [BioC] getGEO and wilcox.test   Sean Davis
• [BioC] getGEO and wilcox.test   Sean Davis
• [BioC] Summing Views on coverage by base   Sean Davis
• [BioC] Summing Views on coverage by base   Sean Davis
• [BioC] Summing Views on coverage by base   Sean Davis
• [BioC] Manually upregulate a gene   Sean Davis
• [BioC] eset from GEOqury pkg   Sean Davis
• [BioC] SRAdb error   Sean Davis
• [BioC] Please help: SNP Frequency Analysis Package in Bioconductor   Sean Davis
• [BioC] Using Anova for microarray data   Sean Davis
• [BioC] Gene-Metabolite correlation network   Sean Davis
• [BioC] Using Anova for microarray data   Sean Davis
• [BioC] LIMMA package - coefficient not estimable   Sean Davis
• [BioC] LIMMA package - coefficient not estimable   Sean Davis
• [BioC] GEOquery Data structure: GSEMatrix   Sean Davis
• [BioC] How to combine different annotation (chromosomic, genic) when using easyRNASeq (was easyRNASeq error)   Davis, Wade
• [BioC] a possible bug of trimLRPatterns   Marcus Davy
• [BioC] an error from ShortRead   Marcus Davy
• [BioC] a possible bug of trimLRPatterns   Marcus Davy
• [BioC] a possible bug of trimLRPatterns   Marcus Davy
• [BioC] A question about MA and RG lists and normalization with two channel agilent arrays.   Marcus Davy
• [BioC] A question about MA and RG lists and normalization with two channel agilent arrays.   Marcus Davy
• [BioC] post-doctoral position   Day, Roger S
• [BioC] easyRNASeq error   Nicolas Delhomme
• [BioC] easyRNASeq error   Nicolas Delhomme
• [BioC] easyRNASeq error   Nicolas Delhomme
• [BioC] easyRNASeq error   Nicolas Delhomme
• [BioC] easyRNASeq error   Nicolas Delhomme
• [BioC] How to combine different annotation (chromosomic, genic) when using easyRNASeq (was easyRNASeq error)   Nicolas Delhomme
• [BioC] Question about hgu133plus2cdf?   Nicolas Delhomme
• [BioC] Question about hgu133plus2cdf?   Nicolas Delhomme
• [BioC] how to map Affymetrix ID to ensemble gene ID   Nicolas Delhomme
• [BioC] how to map Affymetrix ID to ensemble gene ID   Nicolas Delhomme
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Nicolas Delhomme
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Nicolas Delhomme
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Nicolas Delhomme
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Nicolas Delhomme
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Nicolas Delhomme
• [BioC] GAGE heatmap pdf question...   Alan Derr
• [BioC] problems generating a gene2GOlist in topGO   António Miguel de Jesus Domingues
• [BioC] Bioconductor Digest, Vol 109, Issue 14   Pan Du
• [BioC] LumiT VST error   Pan Du
• [BioC] fastest way to get a gene list having certain GO term   Duke
• [BioC] fastest way to get a gene list having certain GO term   Duke
• [BioC] fastest way to get a gene list having certain GO term   Duke
• [BioC] IlluminaMousev2.db probe quality information questions?   Mark Dunning
• [BioC] BiomaRt error: server down?   Steffen Durinck
• [BioC] question about biomaRt problem   Steffen Durinck
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Steffen Durinck
• [BioC] clusterCt {HTqPCR}   Heidi Dvinge
• [BioC] File formats for high throughput qPCR data   Heidi Dvinge
• [BioC] RobustSpline normalization method applied to agilent data   Heidi Dvinge
• [BioC] question about biomaRt problem   Heidi Dvinge
• [BioC] question about biomaRt problem   Heidi Dvinge
• [BioC] HTqPCR: normalizeCtData   Heidi Dvinge
• [BioC] Question about limma package   Anna Dvorkin
• [BioC] cannot allocate vector for random forest   Salwa Eid
• [BioC] FW: cannot allocate vector for random forest   Salwa Eid
• [BioC] can't allocate vector for random forest   Salwa Eid
• [BioC] error using random forest   Salwa Eid
• [BioC] error in using random forest   Salwa Eid
• [BioC] how can i apply random forest to expression sets of dna microarray   Salwa Eid
• [BioC] how can i apply random forest to expression sets of dna microarray   Salwa Eid
• [BioC] GEOquery Data structure: GSEMatrix   Hendrik Falk
• [BioC] ggplot2: changing the axes appearance   Faryabi, Robert (NIH/NCI) [F]
• [BioC] DESeq vs DEXSeq   Robert M. Flight
• [BioC] DESeq vs DEXSeq   Robert M. Flight
• [BioC] svm (e1071) class weighting in a multi-class problem   Javier Pérez Florido
• [BioC] problems using the latest version of e1071 (svm)   Javier Pérez Florido
• [BioC] optimizing class weights in e1071   Javier Pérez Florido
• [BioC] some questions about lumi package and Illumina arrays   Javier Pérez Florido
• [BioC] some questions about lumi package and Illumina arrays   Javier Pérez Florido
• [BioC] cutoff for NUSE plot in oligo   Richard Friedman
• [BioC] GRENITS won't run with example data   Tyler Funnell
• [BioC] variance and coefficient of variation with edgeR   Miguel Gallach
• [BioC] variance and coefficient of variation with edgeR   Miguel Gallach
• [BioC] edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation?   Miguel Gallach
• [BioC] extracting sequence from a genome   Iain Gallagher
• [BioC] extracting sequence from a genome   Iain Gallagher
• [BioC] edgeR-How to obtain a list of normalized expression values   Iain Gallagher
• [BioC] Rgraphviz and node label placement   Iain Gallagher
• [BioC] Affymetrix Intronic Normalization Control Probes Differentially Expressed?   Paul Geeleher
• [BioC] F p.value.adj missing from write.fit/limma   Pascal Gellert
• [BioC] F p.value.adj missing from write.fit/limma   Pascal Gellert
• [BioC] Finding coding SNPs with predictCoding   Thomas Girke
• [BioC] cummeRbund package function diffData returns no rows for TSS features   Loyal A. Goff
• [BioC] cummeRbund package function diffData returns no rows for TSS features   Loyal A. Goff
• [BioC] setting up the correlation matrix with two channel, dye swapped data . How to deal with Bio and Tech replicates?   Richard Green
• [BioC] A question about MA and RG lists and normalization with two channel agilent arrays.   Richard Green
• [BioC] A question about MA and RG lists and normalization with two channel agilent arrays.   Richard Green
• [BioC] Summing Views on coverage by base   Ivan Gregoretti
• [BioC] pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays   Groot, Philip de
• [BioC] RobustSpline normalization method applied to agilent data   Priscila Grynberg
• [BioC] RobustSpline normalization method applied to agilent data   Priscila Grynberg
• [BioC] how to get pig genome and for miRNA target scan   José Afonso Guerra-Assunção
• [BioC] Problem with Bimap objects   Lola Guerrero
• [BioC] How can I access to a gene set   Lola Guerrero
• [BioC] How can I access to a gene set   Lola Guerrero
• [BioC] Finding coding SNPs with predictCoding   Alex Gutteridge
• [BioC] Finding coding SNPs with predictCoding   Alex Gutteridge
• [BioC] how to make line graph   Alex Gutteridge
• [BioC] Need immediate help please-BeadSummaryData   Cute Guy
• [BioC] Gviz question   Hahne, Florian
• [BioC] Problems using arrayQualityMetrics   Syed Haider
• [BioC] Problems using arrayQualityMetrics   Syed Haider
• [BioC] problems installing xcms package   Juliet Hannah
• [BioC] arrayQualityMetrics error and question   Daniel Aaen Hansen
• [BioC] arrayQualityMetrics error and question   Daniel Aaen Hansen
• [BioC] arrayQualityMetrics error with MAList   Daniel Aaen Hansen
• [BioC] arrayQualityMetrics error and question   Daniel Aaen Hansen
• [BioC] arrayQualityMetrics error with MAList   Daniel Aaen Hansen
• [BioC] re incomplete analysis in Deseq   Kasper Daniel Hansen
• [BioC] re incomplete analysis in Deseq   Kasper Daniel Hansen
• [BioC] re incomplete analysis in Deseq   Kasper Daniel Hansen
• [BioC] dead or alive vignette in biomaRt? was: question about biomaRt problem   Kasper Daniel Hansen
• [BioC] New to Bioconductor is there a better way?   Kasper Daniel Hansen
• [BioC] ChIPpeakAnno on pathway enrichment   Yuan Hao
• [BioC] snpStats, read.long, alleles in two columns   Liz Hare
• [BioC] snpStats, read.long, alleles in two columns   Liz Hare
• [BioC] question about makeVennDiagram   Ron Hart
• [BioC] Rsamtools installation   Bruce Hayward
• [BioC] Rsamtools installation   Bruce Hayward
• [BioC] beadarray vignette has broken code in R2.14.1?   Henriquez, Nick
• [BioC] homopolymer gap extension penalty in Biostrings   Noah Hoffman
• [BioC] plotting a CA   Susan Holmes
• [BioC] problem creating own org.Ss.eg.db   Hooiveld, Guido
• [BioC] BiomaRt error: server down?   Lisa Hopcroft
• [BioC] BiomaRt error: server down?   Hans-Rudolf Hotz
• [BioC] eset from GEOqury pkg   Jing Huang
• [BioC] eset from GEOqury pkg   Jing Huang
• [BioC] arrayQualityMetrics error with MAList   Wolfgang Huber
• [BioC] arrayQualityMetrics error with MAList   Wolfgang Huber
• [BioC] arrayQualityMetrics package - bugs and errors   Wolfgang Huber
• [BioC] arrayQualityMetrics error and question   Wolfgang Huber
• [BioC] arrayQualityMetrics error with MAList   Wolfgang Huber
• [BioC] re incomplete analysis in Deseq   Wolfgang Huber
• [BioC] re incomplete analysis in Deseq   Wolfgang Huber
• [BioC] EBImage: Negative pixel intensities?!?   Wolfgang Huber
• [BioC] arrayQualityMetrics error and question   Wolfgang Huber
• [BioC] Checking RNAseq DESeq pipeline   Wolfgang Huber
• [BioC] arrayQualityMetrics error and question   Wolfgang Huber
• [BioC] arrayQualityMetrics error and question   Wolfgang Huber
• [BioC] re incomplete analysis in Deseq   Wolfgang Huber
• [BioC] unable to readImage using EBImage package   Wolfgang Huber
• [BioC] question about biomaRt problem   Wolfgang Huber
• [BioC] for running arrayQualityMetrics   Wolfgang Huber
• [BioC] Error by using gpr data with marray   Wolfgang Huber
• [BioC] dead or alive vignette in biomaRt? was: question about biomaRt problem   Wolfgang Huber
• [BioC] dead or alive vignette in biomaRt? was: question about biomaRt problem   Wolfgang Huber
• [BioC] arrayQualityMetrics error with MAList   Wolfgang Huber
• [BioC] Problems using arrayQualityMetrics   Wolfgang Huber
• [BioC] DeSeq Volcano plot- error   Wolfgang Huber
• [BioC] Problems using arrayQualityMetrics   Wolfgang Huber
• [BioC] Problems using arrayQualityMetrics   Wolfgang Huber
• [BioC] Problems using arrayQualityMetrics   Wolfgang Huber
• [BioC] DESeq estimateDispersion options for lower depth miRNA-seq   Wolfgang Huber
• [BioC] Up & Downregulated genes using DESeq   Wolfgang Huber
• [BioC] DESeq- figures on variance estimation   Wolfgang Huber
• [BioC] Problems installing EBImage package   Wolfgang Huber
• [BioC] DESeq estimateDispersion options for lower depth   Wolfgang Huber
• [BioC] DESeq estimateDispersion options for lower depth miRNA-seq   Wolfgang Huber
• [BioC] Error in reading 450k data using lumiMethyR   Khadeeja Ismail
• [BioC] Coverage Question: GenomicRanges   Lakshmanan Iyer
• [BioC] batch effect confounded with condition   Andrew Jaffe
• [BioC] batch effect confounded with condition   Andrew Jaffe
• [BioC] A problem about trimLRPatterns   Harris A. Jaffee
• [BioC] A problem about trimLRPatterns   Harris A. Jaffee
• [BioC] A problem about trimLRPatterns   Harris A. Jaffee
• [BioC] a problem with trimLRPatterns   Harris A. Jaffee
• [BioC] Filtering genes on highest expression before or after LIMMA?   Ekta Jain
• [BioC] Use probesets with highest baseline expression for differntial gene   Ekta Jain
• [BioC] Up & Downregulated genes using DESeq   Ekta Jain
• [BioC] Up & Downregulated genes using DESeq   Ekta Jain
• [BioC] some questions about lumi package and Illumina arrays   Ekta Jain
• [BioC] DNAcopy for CNV in SNP Affy 6.0   Ekta Jain
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] unable to readImage using EBImage package   Nurdiyanah Jambari
• [BioC] Ensembl and refseq genes   chris Jhon
• [BioC] "charm" for MeDIP?   Johnny
• [BioC] How to choose the most 2 different samples in an array experiment   Maciej Jończyk
• [BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7   Amit Kumar Kashyap
• [BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7   Amit Kumar Kashyap
• [BioC] Three tenure track assistant professorship openings at Inst. Behavioral Genetics, University of Colorado Boulder   Matthew Keller
• [BioC] adding factors to a data frame from a dataframe   Tom Keller
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Rhoda Kinsella
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Rhoda Kinsella
• [BioC] readGappedAlignments, package:GenomicRanges   Milica Krunic
• [BioC] saving GRangesList object; conversion to GFF   Milica Krunic
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Milica Krunic
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Milica Krunic
• [BioC] LumiT VST error   Paolo Kunderfranco
• [BioC] can't get degree function to work in graph package   Burak Kutlu
• [BioC] a way to select and filter edge attributes in RCytoscape   Burak Kutlu
• [BioC] RCytoscape not recognizing initiated edge attributes.   Burak Kutlu
• [BioC] RCytoscape not recognizing initiated edge attributes.   Burak Kutlu
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Burak Kutlu
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Burak Kutlu
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Burak Kutlu
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Burak Kutlu
• [BioC] cummeRbund package function diffData returns no rows for TSS features   Asta Laiho
• [BioC] cummeRbund package function diffData returns no rows for TSS features   Asta Laiho
• [BioC] aCGH segmentation with DNAcopy   Emilie Lalonde
• [BioC] creating GRanges and reading BAM files   Michael Lawrence
• [BioC] creating GRanges and reading BAM files   Michael Lawrence
• [BioC] creating GRanges and reading BAM files   Michael Lawrence
• [BioC] Coverage Question: GenomicRanges   Michael Lawrence
• [BioC] rsbml: problem writing a model to file   Michael Lawrence
• [BioC] rsbml: problem writing a model to file   Michael Lawrence
• [BioC] rsbml: problem writing a model to file   Michael Lawrence
• [BioC] rsbml: problem writing a model to file   Michael Lawrence
• [BioC] rtracklayer export.wig variableStep problem   Michael Lawrence
• [BioC] rtracklayer export.wig variableStep problem   Michael Lawrence
• [BioC] rtracklayer export.wig variableStep problem   Michael Lawrence
• [BioC] saving GRangesList object; conversion to GFF   Michael Lawrence
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Michael Lawrence
• [BioC] RangedData Element Metadata   Michael Lawrence
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Michael Lawrence
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Michael Lawrence
• [BioC] Coverage Question: GenomicRanges   Lax
• [BioC] how to set model.matrix for SVA/ComBat   Jeff Leek
• [BioC] how to set model.matrix for SVA/ComBat   Jeff Leek
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in locateVariants for a GRanges object   Lescai, Francesco
• [BioC] error in using random forest   Steve Lianoglou
• [BioC] re incomplete analysis in Deseq   Steve Lianoglou
• [BioC] re incomplete analysis in Deseq   Steve Lianoglou
• [BioC] re incomplete analysis in Deseq   Steve Lianoglou
• [BioC] svm (e1071) class weighting in a multi-class problem   Steve Lianoglou
• [BioC] A few Q's on using DEXSeq with mucho data   Steve Lianoglou
• [BioC] A few Q's on using DEXSeq with mucho data   Steve Lianoglou
• [BioC] A few Q's on using DEXSeq with mucho data   Steve Lianoglou
• [BioC] how to read empty line in the fastqfile   Steve Lianoglou
• [BioC] fisher exact test pairwise comparisons   Steve Lianoglou
• [BioC] how can i apply random forest to expression sets of dna microarray   Steve Lianoglou
• [BioC] how can i apply random forest to expression sets of dna microarray   Steve Lianoglou
• [BioC] error in locateVariants for a GRanges object   Steve Lianoglou
• [BioC] A few Q's on using DEXSeq with mucho data   Steve Lianoglou
• [BioC] question from any of TopGO, gage, sigpathway, GSVA, GOstat users   Steve Lianoglou
• [BioC] Intersecting two chromosomal ranges but keeping the unique ones   Steve Lianoglou
• [BioC] Intersecting two chromosomal ranges but keeping the unique ones   Steve Lianoglou
• [BioC] DNA sequence analysis question   Steve Lianoglou
• [BioC] Ensembl and refseq genes   Steve Lianoglou
• [BioC] Ensembl and refseq genes   Steve Lianoglou
• [BioC] How to choose the most 2 different samples in an array experiment   Steve Lianoglou
• [BioC] problems using the latest version of e1071 (svm)   Steve Lianoglou
• [BioC] Limma and negative p-values   Steve Lianoglou
• [BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7   Steve Lianoglou
• [BioC] extracting sequence from a genome   Steve Lianoglou
• [BioC] extracting sequence from a genome   Steve Lianoglou
• [BioC] any good R package to scan microRNA target?   Steve Lianoglou
• [BioC] any good R package to scan microRNA target?   Steve Lianoglou
• [BioC] any good R package to scan microRNA target?   Steve Lianoglou
• [BioC] any good R package to scan microRNA target?   Steve Lianoglou
• [BioC] Copy Number Analysis for Mapreduce   Steve Lianoglou
• [BioC] how to write fasta file of RNA sequences   Steve Lianoglou
• [BioC] Affymetrix Intronic Normalization Control Probes Differentially Expressed?   Steve Lianoglou
• [BioC] Manually upregulate a gene   Steve Lianoglou
• [BioC] Up & Downregulated genes using DESeq   Steve Lianoglou
• [BioC] dispatch method   Steve Lianoglou
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Steve Lianoglou
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Steve Lianoglou
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Steve Lianoglou
• [BioC] DESeq multi-factor export results   Ingrid Lindquist
• [BioC] DESeq multi-factor export results   Ingrid Lindquist
• [BioC] creating GRanges and reading BAM files   Sunny Yu Liu
• [BioC] Up & Downregulated genes using DESeq   Sunny Yu Liu
• [BioC] Up & Downregulated genes using DESeq   Sunny Yu Liu
• [BioC] Up & Downregulated genes using DESeq   Sunny Yu Liu
• [BioC] fisher exact test pairwise comparisons   Ann Loraine
• [BioC] qcplot() error in methylumi?   Oliver Lyttleton
• [BioC] question regarding ChIPPeakAnno use   Ma, Xian-Yong
• [BioC] question regarding ChIPPeakAnno use   Ma, Xian-Yong
• [BioC] normalize.invariantset   James W. MacDonald
• [BioC] how to make line graph   James W. MacDonald
• [BioC] how to make line graph   James W. MacDonald
• [BioC] how to rank affy probesets by their probe-effect magnitude   James W. MacDonald
• [BioC] Problem fitting a linear model using limma   James W. MacDonald
• [BioC] Problem fitting a linear model using limma   James W. MacDonald
• [BioC] Problem fitting a linear model using limma   James W. MacDonald
• [BioC] error of justRMA() under Linux   James W. MacDonald
• [BioC] Is this a basic bug or something else ?   James W. MacDonald
• [BioC] limma multiple groups comparison produces different pvalue comparing with two group comparsion   James W. MacDonald
• [BioC] annotate htmlpage error   James W. MacDonald
• [BioC] Question about hgu133plus2cdf?   James W. MacDonald
• [BioC] Affymetrix Intronic Normalization Control Probes Differentially Expressed?   James W. MacDonald
• [BioC] annotate htmlpage error   James W. MacDonald
• [BioC] design and contrast matrix for limma time series without replicates   James W. MacDonald
• [BioC] design and contrast matrix for limma time series without replicates   James W. MacDonald
• [BioC] Duplicate probes   James W. MacDonald
• [BioC] How can I access to a gene set   James W. MacDonald
• [BioC] How can I access to a gene set   James W. MacDonald
• [BioC] Using Anova for microarray data   James W. MacDonald
• [BioC] Updating Package Versions from SVN   James W. MacDonald
• [BioC] F p.value.adj missing from write.fit/limma   James W. MacDonald
• [BioC] biocLite() does not accept 'lib.loc' for updating   Martin Maechler
• [BioC] fisher exact test pairwise comparisons   Alyaa Mahmoud
• [BioC] Z-scores   Alyaa Mahmoud
• [BioC] ChIPpeakAnno - Request of information   Federico Marini
• [BioC] Problem fitting a linear model using limma   Joaquin Martinez
• [BioC] Problem fitting a linear model using limma   Joaquin Martinez
• [BioC] Problem fitting a linear model using limma   Joaquin Martinez
• [BioC] Problem fitting a linear model using limma   Joaquin Martinez
• [BioC] FrozenRMA how to   Matthew McCall
• [BioC] how to rank affy probesets by their probe-effect magnitude   Matthew McCall
• [BioC] how to rank affy probesets by their probe-effect magnitude   Matthew McCall
• [BioC] impute.knn   Ali Mohammadian
• [BioC] normalize.invariantset   Ali Mohammadian
• [BioC] Any code for simulation of qPCR studies?   Ali Mohammadian
• [BioC] clusterCt {HTqPCR}   Ali Mohammadian
• [BioC] question from any of TopGO, gage, sigpathway, GSVA, GOstat users   Ali Mohammadian
• [BioC] How to choose the most 2 different samples in an array experiment   Ali Mohammadian
• [BioC] HTqPCR: normalizeCtData   Ali Mohammadian
• [BioC] Up & Downregulated genes using DESeq   Bruce Moran(External)
• [BioC] Biobase typo in example of AnnotatedDataFrame man page   Martin Morgan
• [BioC] KEGGSOAP   Martin Morgan
• [BioC] report a possible bug of   Martin Morgan
• [BioC] can't allocate vector for random forest   Martin Morgan
• [BioC] GSVA with entrez ids?   Martin Morgan
• [BioC] error using random forest   Martin Morgan
• [BioC] error in using random forest   Martin Morgan
• [BioC] Problem installing GenomicFeatures   Martin Morgan
• [BioC] how to read empty line in the fastqfile   Martin Morgan
• [BioC] Problem installing GenomicFeatures   Martin Morgan
• [BioC] how to read empty line in the fastqfile   Martin Morgan
• [BioC] a possible bug of trimLRPatterns   Martin Morgan
• [BioC] error in locateVariants for a GRanges object   Martin Morgan
• [BioC] error in locateVariants for a GRanges object   Martin Morgan
• [BioC] error in locateVariants for a GRanges object   Martin Morgan
• [BioC] breastCancerMAINZ package installation problem   Martin Morgan
• [BioC] annotate htmlpage error   Martin Morgan
• [BioC] Summing Views on coverage by base   Martin Morgan
• [BioC] Summing Views on coverage by base   Martin Morgan
• [BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7   Martin Morgan
• [BioC] Error when using impute to get missing values   Martin Morgan
• [BioC] Rsamtools installation   Martin Morgan
• [BioC] GRENITS won't run with example data   Edward Morrissey
• [BioC] oligonucleotideTransitions from Biostrings package   Muino, Jose
• [BioC] BioMart server down yesterday and today? Error   Adriana Munoz
• [BioC] BioMart server down yesterday and today? Error   Adriana Munoz
• [BioC] Affymetrix Intronic Normalization Control Probes Differentially Expressed?   Alexandra Muñoz
• [BioC] Pre-filtering before differential expression analysis in LIMMA   Karthik K N
• [BioC] Is the qrqc package source updated?   NDowell
• [BioC] Finding coding SNPs with predictCoding   Valerie Obenchain
• [BioC] countOverlaps within Mode Counting   Valerie Obenchain
• [BioC] summarizeOverlaps vs countOverlaps   Valerie Obenchain
• [BioC] Finding coding SNPs with predictCoding   Valerie Obenchain
• [BioC] Finding coding SNPs with predictCoding   Valerie Obenchain
• [BioC] error in locateVariants for a GRanges object   Valerie Obenchain
• [BioC] error in locateVariants for a GRanges object   Valerie Obenchain
• [BioC] Copy number analysis   Valerie Obenchain
• [BioC] distanceToNearest for GRanges?   Valerie Obenchain
• [BioC] Looks like a bug in GenomicRanges::.breakTie   Valerie Obenchain
• [BioC] Looks like a bug in GenomicRanges::.breakTie   Valerie Obenchain
• [BioC] batch effect confounded with condition   Moshe Olshansky
• [BioC] Problem installing GenomicFeatures   Georg Otto
• [BioC] Problem installing GenomicFeatures   Georg Otto
• [BioC] Problem installing GenomicFeatures   Georg Otto
• [BioC] annotate htmlpage error   Georg Otto
• [BioC] annotate htmlpage error   Georg Otto
• [BioC] how to get gene list for given GO terms?   Ou, Jianhong
• [BioC] how to get gene list for given GO terms?   Ou, Jianhong
• [BioC] question regarding ChIPPeakAnno use   Ou, Jianhong
• [BioC] question regarding ChIPPeakAnno use   Ou, Jianhong
• [BioC] ChIPpeakAnno - Request of information   Ou, Jianhong
• [BioC] homopolymer gap extension penalty in Biostrings   Hervé Pagès
• [BioC] homopolymer gap extension penalty in Biostrings   Hervé Pagès
• [BioC] creating GRanges and reading BAM files   Hervé Pagès
• [BioC] creating GRanges and reading BAM files   Hervé Pagès
• [BioC] creating GRanges and reading BAM files   Hervé Pagès
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Hervé Pagès
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Hervé Pagès
• [BioC] readGappedAlignments, package:GenomicRanges   Hervé Pagès
• [BioC] readGappedAlignments, package:GenomicRanges   Hervé Pagès
• [BioC] an erro related with RNAStringSet   Hervé Pagès
• [BioC] New to Bioconductor is there a better way?   Hervé Pagès
• [BioC] how to map Affymetrix ID to ensemble gene ID   Hervé Pagès
• [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart   Hervé Pagès
• [BioC] Summing Views on coverage by base   Hervé Pagès
• [BioC] Summing Views on coverage by base   Hervé Pagès
• [BioC] Summing Views on coverage by base   Hervé Pagès
• [BioC] curious IRanges error when sort()ing a GRanges   Hervé Pagès
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Hervé Pagès
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Hervé Pagès
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Hervé Pagès
• [BioC] Ensembl gene ids corresponding to affymetrix rat exon array transcript level ids   James Perkins
• [BioC] (no subject)   James Perkins
• [BioC] FrozenRMA how to   Alejandro Sánchez Pla
• [BioC] Newer version of DESeq give much small list of DE genes   Abhishek Pratap
• [BioC] Looks like a bug in GenomicRanges::.breakTie   Paul Theodor Pyl
• [BioC] classify SNPs   Kunbin Qu
• [BioC] edgeR: tag vs abundance plot   Alpesh Querer
• [BioC] can't allocate vector for random forest   Alpesh Querer
• [BioC] LIMMA - summarization   Kripa R
• [BioC] LIMMA - summarization of Illumina probes for same gene   Kripa R
• [BioC] 13th MRC Social, Genetic & Developmental Psychiatry SUMMER SCHOOL 18th - 22th June 2012   Ramasamy, Adaikalavan
• [BioC] calcNormFactors()   Anand K S Rao
• [BioC] Difficulty in AnnotatedDataFrame   James F. Reid
• [BioC] Difficulty in AnnotatedDataFrame   James F. Reid
• [BioC] Biobase typo in example of AnnotatedDataFrame man page   James F. Reid
• [BioC] eset from GEOqury pkg   James F. Reid
• [BioC] eset from GEOqury pkg   James F. Reid
• [BioC] calcNormFactors()   Mark Robinson
• [BioC] homopolymer gap extension penalty in Biostrings   Frederick Ross
• [BioC] GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa   Javerjung Sandhu
• [BioC] GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa   Javerjung Sandhu
• [BioC] SNP Frequency Analysis Package in Bioconductor   Javerjung Sandhu
• [BioC] Please help: SNP Frequency Analysis Package in Bioconductor   Javerjung Sandhu
• [BioC] Intersecting two chromosomal ranges but keeping the unique ones   Yadav Sapkota
• [BioC] Intersecting two chromosomal ranges but keeping the unique ones   Yadav Sapkota
• [BioC] Copy number analysis   Robert Scharpf
• [BioC] rtracklayer export.wig variableStep problem   Vincent Schulz
• [BioC] can't get degree function to work in graph package   Paul Shannon
• [BioC] DNA sequence analysis question   Paul Shannon
• [BioC] a way to select and filter edge attributes in RCytoscape   Paul Shannon
• [BioC] RCytoscape not recognizing initiated edge attributes.   Paul Shannon
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Paul Shannon
• [BioC] problem getting setNodeColorRule from RCytoscape to work   Paul Shannon
• [BioC] initializing RCy node & edge attributes [was Re: problem getting setNodeColorRule from RCytoscape to work]   Paul Shannon
• [BioC] limma multiple groups comparison produces different pvalue comparing with two group comparsion   Shao, Chunxuan
• [BioC] limma multiple groups comparison produces different pvalue comparing with two group comparsion   Shao, Chunxuan
• [BioC] design and contrast matrix for limma time series without replicates   Chunxuan Shao
• [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq   Wei Shi
• [BioC] some questions about lumi package and Illumina arrays   Wei Shi
• [BioC] GSVA with entrez ids?   Ed Siefker
• [BioC] Duplicate probes   Ed Siefker
• [BioC] KEGGSOAP   Ricardo Silva
• [BioC] KEGGSOAP   Ricardo Silva
• [BioC] KEGGSOAP   Ricardo Silva
• [BioC] KEGGSOAP   Ricardo Silva
• [BioC] plotting a ca.   Aaral Singh
• [BioC] Manually upregulate a gene   Reema Singh
• [BioC] Problems using arrayQualityMetrics   Reema Singh
• [BioC] how edgeR control outliers?   Gordon K Smyth
• [BioC] Filtering genes on highest expression before or after LIMMA?   Gordon K Smyth
• [BioC] Summarizing Single-channel Agilent data   Gordon K Smyth
• [BioC] how edgeR control outliers?   Gordon K Smyth
• [BioC] Summarizing Single-channel Agilent data   Gordon K Smyth
• [BioC] RobustSpline normalization method applied to agilent data   Gordon K Smyth
• [BioC] LIMMA - summarization of Illumina probes for same gene   Gordon K Smyth
• [BioC] LIMMA - summarization of Illumina probes for same gene   Gordon K Smyth
• [BioC] Pre-filtering before differential expression analysis in LIMMA   Gordon K Smyth
• [BioC] edgeR i get 377 significant genes where in DESeq i got 0   Gordon K Smyth
• [BioC] edgeR i get 377 significant genes where in DESeq i got 0   Gordon K Smyth
• [BioC] Alert to developers about changes to edgeR   Gordon K Smyth
• [BioC] edgeR: Specifying the "coef"-argument in glmLRT in a two factor study   Gordon K Smyth
• [BioC] edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation   Gordon K Smyth
• [BioC] dispatch method   Stefanie
• [BioC] dispatch method   Stefanie
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Stefanie
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Stefanie
• [BioC] countOverlaps within Mode Counting   Dario Strbenac
• [BioC] RangedData Element Metadata   Dario Strbenac
• [BioC] Fw: Warning of function "ncbiTaxonomy"   Chris Stubben
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] beadarray vignette has broken code in R2.14.1?   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] arrayQualityMetrics error and question   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] EBImage in R-Cloud   Dan Tenenbaum
• [BioC] unable to readImage using EBImage package   Dan Tenenbaum
• [BioC] can't get degree function to work in graph package   Dan Tenenbaum
• [BioC] cummeRbund loading error   Dan Tenenbaum
• [BioC] Rgraphiz   Dan Tenenbaum
• [BioC] biocLite() does not accept 'lib.loc' for updating   Dan Tenenbaum
• [BioC] Is the qrqc package source updated?   Dan Tenenbaum
• [BioC] BioMart server down yesterday and today? Error   Dan Tenenbaum
• [BioC] BioMart server down yesterday and today? Error   Dan Tenenbaum
• [BioC] SRAdb error   Dan Tenenbaum
• [BioC] problems installing xcms package   Dan Tenenbaum
• [BioC] Cevap: Re: SRAdb error   Dan Tenenbaum
• [BioC] Updating Package Versions from SVN   Dan Tenenbaum
• [BioC] beadarray package: BASH error   Dan Tenenbaum
• [BioC] Fwd: beadarray package: BASH error   Dan Tenenbaum
• [BioC] JOB: Research Associate in Statistical Epigenomics (London)   Andrew Teschendorff
• [BioC] how edgeR control outliers?   Yuan Tian
• [BioC] how edgeR control outliers?   Yuan Tian
• [BioC] reading with lumi   Tim Triche, Jr.
• [BioC] cannot allocate vector for random forest   Tim Triche, Jr.
• [BioC] impute.knn   Tim Triche, Jr.
• [BioC] classify SNPs   Tim Triche, Jr.
• [BioC] plotting a CA   Tim Triche, Jr.
• [BioC] plotting a CA   Tim Triche, Jr.
• [BioC] batch effect confounded with condition   Tim Triche, Jr.
• [BioC] extracting sequence from a genome   Tim Triche, Jr.
• [BioC] extracting sequence from a genome   Tim Triche, Jr.
• [BioC] How to choose the most 2 different samples in an array experiment   Tim Triche, Jr.
• [BioC] qcplot() error in methylumi?   Tim Triche, Jr.
• [BioC] rtracklayer export.wig variableStep problem   Tim Triche, Jr.
• [BioC] Error when using impute to get missing values   Tim Triche, Jr.
• [BioC] Adjacency to network using R   Tim Triche, Jr.
• [BioC] Adjacency to network using R   Tim Triche, Jr.
• [BioC] Adjacency to network using R   Tim Triche, Jr.
• [BioC] rtracklayer export.wig variableStep problem   Tim Triche, Jr.
• [BioC] Using Anova for microarray data   Tim Triche, Jr.
• [BioC] curious IRanges error when sort()ing a GRanges   Tim Triche, Jr.
• [BioC] curious IRanges error when sort()ing a GRanges   Tim Triche, Jr.
• [BioC] Up & Downregulated genes using DESeq   Tim Triche, Jr.
• [BioC] Question about hgu133plus2cdf?   Fabrice Tourre
• [BioC] Question about hgu133plus2cdf?   Fabrice Tourre
• [BioC] Gene-Metabolite correlation network   B Usadel
• [BioC] Gene-Metabolite correlation network   B Usadel
• [BioC] Gene-Metabolite correlation network   B Usadel
• [BioC] Help with lumi R package   Minyue Wang
• [BioC] edgeR MDS plot   Lina Weber
• [BioC] GAGE heatmap pdf question...   Luo Weijun
• [BioC] GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa   Luo Weijun
• [BioC] Summarizing Single-channel Agilent data   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] arrayQualityMetrics error and question   David Westergaard
• [BioC] how to map Affymetrix ID to ensemble gene ID   David Westergaard
• [BioC] how to map Affymetrix ID to ensemble gene ID   David Westergaard
• [BioC] Error when using impute to get missing values   David Westergaard
• [BioC] DESeq for two-factor models   Henning Wildhagen
• [BioC] edgeR: Specifying the "coef"-argument in glmLRT in a two factor study   Henning Wildhagen
• [BioC] limma package topTable error   Monica Wong
• [BioC] ChIPpeakAnno findVennCounts   Ying Wu
• [BioC] SRAdb error   Ayten YIGITER
• [BioC] ggplot2: changing the axes appearance   Tengfei Yin
• [BioC] distanceToNearest for GRanges?   Janet Young
• [BioC] distanceToNearest for GRanges?   Janet Young
• [BioC] making use of the Apis mellifera BeeBase assembly 4 data in goseq   Matthew Young
• [BioC] crlmm and Affymetrix SNP5 array [genotyping issues]   Ali ZAIDI
• [BioC] survival prediction from multiple genes   Ahmet ZEHIR
• [BioC] Job Announcement: Genome Informatics   Zadeh, Jenny Drnevich
• [BioC] 2 more Job Announcements   Zadeh, Jenny Drnevich
• [BioC] flip strand information in GappedAlignments or GRangesList Object   Kathi Zarnack
• [BioC] PPDE results with 'NA' for the web Cyber-t   Li Zhang
• [BioC] PPDE results with 'NA' for the web Cyber-t   Li Zhang
• [BioC] ChIPpeakAnno: Inquiry for Worm Analysis   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno: Inquiry for Worm Analysis   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno as.data.frame error   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno as.data.frame error   Zhu, Lihua (Julie)
• [BioC] ChipPeakAnno question about file conversion   Zhu, Lihua (Julie)
• [BioC] question about makeVennDiagram   Zhu, Lihua (Julie)
• [BioC] question about makeVennDiagram   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno on pathway enrichment   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno: makeVennDiagram and sampling peaks   Zhu, Lihua (Julie)
• [BioC] question regarding ChIPPeakAnno use   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno findVennCounts   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno findVennCounts   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno - Request of information   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno: Inquiry for Worm Analysis   Zhu, Lihua (Julie)
• [BioC] chi-squared   Aaral [guest]
• [BioC] cummeRbund package function diffData returns no rows for TSS features   Asta Laiho [guest]
• [BioC] oligo package: extracting position, sequence, and intensity from Affymetrix tiling array   Cindy [guest]
• [BioC] How to include external applications in package vignette code?   Dave Gerrard [guest]
• [BioC] Question about Normalization   James [guest]
• [BioC] AnnotationDbi - makeOrgPackageFromNCBI - gene_info table is not populated   Jiri Voller [guest]
• [BioC] makeOrgPackageFromNCBI another error - reversed commands   Jiri Voller [guest]
• [BioC] re incomplete analysis in Deseq   Julian [guest]
• [BioC] beadarray package: BASH error   Kemal Akat [guest]
• [BioC] R course: London, Monday 18th - Friday 22nd June 2012.   Leo Schalkwyk [guest]
• [BioC] Problems installing EBImage package   Marco Sassi [guest]
• [BioC] fitmaanova   Maxime Deraspe [guest]
• [BioC] R is the most popular programming language in Bioinformatics   Michael Barton [guest]
• [BioC] EBImage in R-Cloud   Nicole [guest]
• [BioC] Copy number analysis   Raj [guest]
• [BioC] cummeRbund loading error   SC [guest]
• [BioC] Error by using gpr data with marray   Sandra Heise [guest]
• [BioC] Get negative control probes in lumiBarnes data set   Sandra Plancade [guest]
• [BioC] plotting a CA   aoife [guest]
• [BioC] unable to readImage using EBImage package   diyanah [guest]
• [BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"   henlen [guest]
• [BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"   henlen [guest]
• [BioC] edgeR i get 377 significant genes where in DESeq i got 0   papori [guest]
• [BioC] NOISeq-real input parameters   papori [guest]
• [BioC] question about biomaRt problem   rong [guest]
• [BioC] Summarizing Single-channel Agilent data   axel.klenk at actelion.com
• [BioC] Problem with Bimap objects   axel.klenk at actelion.com
• [BioC] DNA sequence analysis question   andigoni
• [BioC] choosing explanatory variables for linear model in limma   somnath bandyopadhyay
• [BioC] summarizeOverlaps vs countOverlaps   swaraj basu
• [BioC] IRAnges compile error   Francoise.LECOMTE at biogemma.com
• [BioC] Gene-Metabolite correlation network   pankaj borah
• [BioC] Gene-Metabolite correlation network   pankaj borah
• [BioC] Adjacency to network using R   pankaj borah
• [BioC] Adjacency to network using R   pankaj borah
• [BioC] Gene-Metabolite correlation network   pankaj borah
• [BioC] Adjacency to network using R   pankaj borah
• [BioC] Using Anova for microarray data   konika chawla
• [BioC] Using Anova for microarray data   konika chawla
• [BioC] Using Anova for microarray data   konika chawla
• [BioC] Using Anova for microarray data   konika chawla
• [BioC] how to set model.matrix for SVA/ComBat   ying chen
• [BioC] how to set model.matrix for SVA/ComBat   ying chen
• [BioC] LIMMA package - coefficient not estimable   yeeling chong
• [BioC] Updating Package Versions from SVN   chris_utah
• [BioC] design and contrast matrix for limma time series without replicates   shao chunxuan
• [BioC] how to make line graph   Dana.Stanley at csiro.au
• [BioC] how to make line graph   Dana.Stanley at csiro.au
• [BioC] how to make line graph   Dana.Stanley at csiro.au
• [BioC] how to make line graph   Dana.Stanley at csiro.au
• [BioC] plotting a CA   aedin culhane
• [BioC] plotting a CA   aedin culhane
• [BioC] plotting a CA   aedin culhane
• [BioC] plotting a CA   aoife doherty
• [BioC] plotting a CA   aoife doherty
• [BioC] plotting a CA   aoife doherty
• [BioC] plotting a CA   aoife doherty
• [BioC] plotting a ca.   aoife doherty
• [BioC] plotting a ca.   aoife doherty
• [BioC] plotting a CA   aoife doherty
• [BioC] Duplicate probes   J.delasHeras at ed.ac.uk
• [BioC] rsbml: problem writing a model to file   hettling
• [BioC] rsbml: problem writing a model to file   hettling
• [BioC] rsbml: problem writing a model to file   hettling
• [BioC] Error in reading 450k data using lumiMethyR   khadeeja ismail
• [BioC] Genetic coding impact on variant calling   John linux-user
• [BioC] copyCountSegments(fit) failed exomeCopy   John linux-user
• [BioC] copyCountSegments(fit) failed exomeCopy   love
• [BioC] DESeq without replicates, Problem trying to obtain significant hits   Melissa.Martin at lshtm.ac.uk
• [BioC] DeSeq Volcano plot- error   Melissa.Martin at lshtm.ac.uk
• [BioC] DESeq- figures on variance estimation   Melissa.Martin at lshtm.ac.uk
• [BioC] plot axis in pROC   David martin
• [BioC] Checking RNAseq DESeq pipeline   nathalie
• [BioC] A problem about trimLRPatterns   wang peter
• [BioC] A problem about trimLRPatterns   wang peter
• [BioC] how to read empty line in the fastqfile   wang peter
• [BioC] a possible bug of trimLRPatterns   wang peter
• [BioC] a problem with trimLRPatterns   wang peter
• [BioC] how to get pig genome and for miRNA target scan   wang peter
• [BioC] how to get pig genome and for miRNA target scan   wang peter
• [BioC] how to get pig genome and for miRNA target scan   wang peter
• [BioC] an error from ShortRead   wang peter
• [BioC] an error from ShortRead   wang peter
• [BioC] any good R package to scan microRNA target?   wang peter
• [BioC] any good R package to scan microRNA target?   wang peter
• [BioC] any good R package to scan microRNA target?   wang peter
• [BioC] an erro related with RNAStringSet   wang peter
• [BioC] how to map Affymetrix ID to ensemble gene ID   wang peter
• [BioC] how to write fasta file of RNA sequences   wang peter
• [BioC] biomaRt cannot find getAffyArrays function   wang peter
• [BioC] how to map Affymetrix ID to ensemble gene ID   wang peter
• [BioC] how to map Affymetrix ID to ensemble gene ID   wang peter
• [BioC] how to map Affymetrix ID to ensemble gene ID   wang peter
• [BioC] arrayQualityMetrics error with MAList   karen power
• [BioC] batch effect confounded with condition   tefina
• [BioC] batch effect confounded with condition   tefina
• [BioC] batch effect confounded with condition   tefina
• [BioC] Fw: Warning of function "ncbiTaxonomy"   wuchunyan
• [BioC] Warning of function "ncbiTaxonomy"   wuchunyan
• [BioC] error of justRMA() under Linux   cao zongfu
• [BioC] Rgraphiz   zahra / زهرا ghayyomi / قیومی

Last message date: Sat Mar 31 17:04:59 CEST 2012
Archived on: Sat Mar 31 17:05:16 CEST 2012

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