April 2013 Archives by author

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Starting: Mon Apr 1 11:18:45 CEST 2013
Ending: Tue Apr 30 23:06:09 CEST 2013
Messages: 520

• [BioC] CfP: CAMDA 2013 - 12th International Conference on Critical Assessment of Massive Data Analysis   CAMDA 2013
• [BioC] Problem in Gap Filling in Metabolic networks   Ahmad
• [BioC] edgeR asimmetry in miRNA experiment   Genomnia - Guffanti Alessandro
• [BioC] topGO Fisher test error   Adrian Alexa
• [BioC] question about using exomeCopy on a single exome sample   Guru Ananda
• [BioC] DESeq estimateDispersions   Simon Anders
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Simon Anders
• [BioC] DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood   Simon Anders
• [BioC] DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood   Simon Anders
• [BioC] FW: DESeq Design (val1 vs mean (val2, val3, val4))   Simon Anders
• [BioC] ★ Bioconductor, Luis Zapata te ha dejado un mensaje   Badoo
• [BioC] Question regarding cellhts2 output   Joseph Barry
• [BioC] Question regarding cellhts2 output   Joseph Barry
• [BioC] Question regarding cellhts2 output   Joseph Barry
• [BioC] Deleting object rows while looping   Daniel Berner
• [BioC] Deleting object rows while looping - II   Daniel Berner
• [BioC] Problem reading VCF file using readVcf from package VariantAnnotation   Ulrich Bodenhofer
• [BioC] Problem reading VCF file using readVcf from package VariantAnnotation   Ulrich Bodenhofer
• [BioC] QuasR special case alignment   Ugo Borello
• [BioC] QuasR special case alignment   Ugo Borello
• [BioC] adj.P metod = \"BH\" many exact the same value   Bas ter Braak
• [BioC] adj.P metod = \"BH\" many exact the same value   Bas ter Braak
• [BioC] EdgeR additive linear model, errors   Colleen Burge
• [BioC] EdgeR additive linear model, errors   Colleen Burge
• [BioC] EdgeR additive linear model, errors   Colleen Burge
• [BioC] sigGeneSet gage function   Vincenzo Capece
• [BioC] How to best include hyperparameter optimization in MLInterfaces?   Vincent Carey
• [BioC] GO term as "keytype" in GO.db   Vincent Carey
• [BioC] GO terms: Annotation for HumanMethylation450   Marc Carlson
• [BioC] subscript out of bounds in makeAnnDbPkg function   Marc Carlson
• [BioC] Mus.musculus package pdf not found   Marc Carlson
• [BioC] GO terms: Annotation for HumanMethylation450   Marc Carlson
• [BioC] GO terms: Annotation for HumanMethylation450   Marc Carlson
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Marc Carlson
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Marc Carlson
• [BioC] Bioconductor and the Google Summer of Code   Marc Carlson
• [BioC] an error in AnnotationForge   Marc Carlson
• [BioC] Add new affy organism platform   Marc Carlson
• [BioC] Affymetrix CEL files   Benilton Carvalho
• [BioC] nsFilter error in genefilter   Robert Castelo
• [BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)   Robert Castelo
• [BioC] GO term as "keytype" in GO.db   Robert Castelo
• [BioC] MEDIPS   Lukas Chavez
• [BioC] MEDIPS error extending reads   Lukas Chavez
• [BioC] MEDIPS error extending reads   Lukas Chavez
• [BioC] MEDIPS error extending reads   Lukas Chavez
• [BioC] MEDIPS error extending reads   Lukas Chavez
• [BioC] nsFilter error in genefilter   Yauheniya Cherkas
• [BioC] nsFilter error in genefilter   Yauheniya Cherkas
• [BioC] nsFilter error in genefilter   Yauheniya Cherkas
• [BioC] [R] Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY   Mete Civelek
• [BioC] EdgeR 'average' cpm   Anna Esteve Codina
• [BioC] Limma linear models   Cornish, Joseph (NIH/NIAID) [F]
• [BioC] goseq error messsage   Nadia Davidson
• [BioC] illimna genes expression file to be imported   Sean Davis
• [BioC] GEOquery not parsing GSE expression sets   Sean Davis
• [BioC] GEOquery not parsing GSE expression sets   Sean Davis
• [BioC] Finding mismatches between reads and reference sequence   Sean Davis
• [BioC] Finding mismatches between reads and reference sequence   Sean Davis
• [BioC] need help for the study design of a RNA-Seq project   Sean Davis
• [BioC] Question about edgeR   Sean Davis
• [BioC] it is strange that I cannot get the fpkm by using easyRNASeq   Nicolas Delhomme
• [BioC] Error loading customCDFs for Bioconductor   Max Diehn
• [BioC] Bug in biocLite?   Pan Du
• [BioC] Lumi problem - 'Annotation columns not available'   Pan Du
• [BioC] Lumi problem - 'Annotation columns not available'   Pan Du
• [BioC] Lumi problem - 'Annotation columns not available'   Pan Du
• [BioC] beadarray package   Mark Dunning
• [BioC] [methylumi] concerning methylumi.bgcorr function and out-of-band intensities   Hannah Elliott
• [BioC] Quantiles from virtualArray example without batcheffect removal are all the same   Daniel Emden
• [BioC] illimna genes expression file to be imported   Marco Fabbri
• [BioC] EdgeR - generating appropriate design and contrast matrix : multi-factorial experiment   Zaki Fadlullah
• [BioC] DEXSeq dexseq_prepare_annotation.py error   Mates Fendrych
• [BioC] PREDA package missing   Francesco Ferrari
• [BioC] PREDA package missing   Francesco Ferrari
• [BioC] Help with flowCore   Finak, Greg
• [BioC] EBImage: Minimum and Maximum intensity on the edge of an object   Bernd Fischer
• [BioC] rhd5 reading variable-length strings   Bernd Fischer
• [BioC] xps- not being able to load it   Andreia Fonseca
• [BioC] nsfilter error from expressionset obtained after using aroma for processing   Andreia Fonseca
• [BioC] error and warning message with blocked samples with Limma   Richard Friedman
• [BioC] error and warning message with blocked samples with Limma I AM STILL HAVING DIFFICULTY   Richard Friedman
• [BioC] How to use 'ebayes' for small samples?   Paul Geeleher
• [BioC] spline example from limma user's guide   Paul Geeleher
• [BioC] transform gwaa.data (Genabel) to snp.matrix (chopsticks)   Paul Geeleher
• [BioC] Microarray Analysis of Rat Gene 2.0 ST arrays   Paul Geeleher
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Paul Geeleher
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Thomas Girke
• [BioC] BitSeq transcript IDs   Peter Glaus
• [BioC] Error installing impute package   Stephanie M. Gogarten
• [BioC] GWATools use in creating ncdf files   Stephanie M. Gogarten
• [BioC] Affymetrix CEL files   Stephanie M. Gogarten
• [BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)   Alvaro J. González
• [BioC] edgeR: Using ratios (translational efficiencies) as input   Alvaro J. González
• [BioC] Finding mismatches between reads and reference sequence   David Greber
• [BioC] Finding mismatches between reads and reference sequence   David Greber
• [BioC] spass im Bett?   Dr. Teresia Gutfeld
• [BioC] Troubles with IdeogramTrack   Deisy Gysi
• [BioC] ReportingTools error   Jason Hackney
• [BioC] ReportingTools error   Jason Hackney
• [BioC] ReportingTools error   Jason Hackney
• [BioC] logFC in GLM of egdeR   Xinwei Han
• [BioC] logFC in GLM of egdeR   Xinwei Han
• [BioC] spline example from limma user's guide   Juliet Hannah
• [BioC] MA plots and assumptions   Juliet Hannah
• [BioC] using offsets from EDASeq and cqn for edgeR   Kasper Daniel Hansen
• [BioC] using offsets from EDASeq and cqn for edgeR   Kasper Daniel Hansen
• [BioC] Questions about the MINFI package:   Kasper Daniel Hansen
• [BioC] BiocInstaller on R-devel   Kasper Daniel Hansen
• [BioC] BiocInstaller on R-devel   Kasper Daniel Hansen
• [BioC] Design matrix and BCV   Manoj Hariharan
• [BioC] Design matrix and BCV   Manoj Hariharan
• [BioC] RNASeqPower   Hart, Steven N., Ph.D.
• [BioC] need help for the study design of a RNA-Seq project   Moritz Hess
• [BioC] GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Jinyan Huang
• [BioC] nsfilter error from expressionset obtained after using aroma for processing   Wolfgang Huber
• [BioC] Cross-posting (was: brief quesion on DESeq2)   Wolfgang Huber
• [BioC] Mass spectrometry data analysis   Wolfgang Huber
• [BioC] rhd5 reading variable-length strings   Wolfgang Huber
• [BioC] MA plots and assumptions   Wolfgang Huber
• [BioC] Postdoc RNA-Interactome at EMBL   Wolfgang Huber
• [BioC] edgeR: Using ratios (translational efficiencies) as input   Wolfgang Huber
• [BioC] identifying drosophila miRNA targets   Fiona Ingleby
• [BioC] GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   Robert Ivanek
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Robert Ivanek
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Robert Ivanek
• [BioC] Troubles with IdeogramTrack   Robert Ivánek
• [BioC] Add new affy organism platform   Ekta Jain
• [BioC] Bioconductor Digest, Vol 122, Issue 5   Johnson, William Evan
• [BioC] ComBat:   Johnson, William Evan
• [BioC] ComBat - question about normalization method   Johnson, William Evan
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results   Maciej Jończyk
• [BioC] [R] Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY   Atul Kakrana
• [BioC] Limma - Result output - Error - Help   Atul Kakrana
• [BioC] Problem with Limma - Possible Limma/affy bug - minimal code not working   Atul Kakrana
• [BioC] Problem with Limma - Possible Limma/affy bug - minimal code not working - Solved - Minor doubt   Atul Kakrana
• [BioC] Problem with Limma - Possible Limma/affy bug - minimal code not working - Solved - Minor doubt   Atul Kakrana
• [BioC] Lumi problem - 'Annotation columns not available'   Atul Kakrana
• [BioC] Lumi problem - 'Annotation columns not available'   Atul Kakrana
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results   Atul Kakrana
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy   Atul Kakrana
• [BioC] Lumi/Limma - Get nuIDs and expression intensities in result   Atul Kakrana
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy   Atul Kakrana
• [BioC] EBImage: Minimum and Maximum intensity on the edge of an object   Kevin
• [BioC] EBImage: remove objects on the edge of an image.   Kevin
• [BioC] Question on unbalanced paired design   Sandhya Pemmasani Kiran
• [BioC] cn.mops: copy number for low-coverage bam files?   Günter Klambauer
• [BioC] transport mcols from one GRange obejct to another   Wim Kreinen
• [BioC] transport mcols from one GRange obejct to another   Wim Kreinen
• [BioC] BitSeq transcript IDs   Maayan Kreitzman
• [BioC] BitSeq getDE   Maayan Kreitzman
• [BioC] MEDIPS   Paolo Kunderfranco
• [BioC] Error installing impute package   Peter Langfelder
• [BioC] Error installing impute package   Peter Langfelder
• [BioC] Error installing (some) Bioconductor packages on Mac OSX under R-3.0.0?   Peter Langfelder
• [BioC] Error installing (some) Bioconductor packages on Mac OSX under R-3.0.0?   Peter Langfelder
• [BioC] rtracklayer importing gtf files   Michael Lawrence
• [BioC] rtracklayer importing gtf files   Michael Lawrence
• [BioC] rtracklayer importing gtf files   Michael Lawrence
• [BioC] expand() vcf with no info columns   Michael Lawrence
• [BioC] GRanges() and naming of metadata columns has changed   Michael Lawrence
• [BioC] GRanges() and naming of metadata columns has changed   Michael Lawrence
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Michael Lawrence
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Michael Lawrence
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Michael Lawrence
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Michael Lawrence
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Michael Lawrence
• [BioC] Potential bug in package("rtracklayer") undefined symbol regcompA   Michael Lawrence
• [BioC] DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood   Kevin Lee
• [BioC] DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood   Kevin Lee
• [BioC] ExomeCopy error   Kevin Lee
• [BioC] ExomeCopy error   Kevin Lee
• [BioC] Finding mismatches between reads and reference sequence   Paul Leo
• [BioC] [Rd] R/Sweave/cairo/freetype bug fix.   Hin-Tak Leung
• [BioC] adj.P metod = \"BH\" many exact the same value   Steve Lianoglou
• [BioC] snp coordinates   Steve Lianoglou
• [BioC] brief quesion on DESeq2   Steve Lianoglou
• [BioC] number of sequence from readfastq   Steve Lianoglou
• [BioC] GO enrichment on an ordered list of genes   Steve Lianoglou
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Steve Lianoglou
• [BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion   Steve Lianoglou
• [BioC] Deleting object rows while looping   Steve Lianoglou
• [BioC] Deleting object rows while looping   Steve Lianoglou
• [BioC] problem installing GenomicFeatures   Steve Lianoglou
• [BioC] Deleting object rows while looping - II   Steve Lianoglou
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy   Steve Lianoglou
• [BioC] Possible Bugs in Contrasts Design of edgeR   Yang Liu
• [BioC] brief quesion on DESeq2   Michael Love
• [BioC] adj.P metod = \"BH\" many exact the same value   Michael Love
• [BioC] deseq2   Michael Love
• [BioC] brief quesion on DESeq2   Michael Love
• [BioC] DESeq: computing 95% CI for negative binomial distribution ?   Michael Love
• [BioC] Interpreting DESeq2 results   Michael Love
• [BioC] DESeq: computing 95% CI for negative binomial distribution ?   Michael Love
• [BioC] DESeq2   Michael Love
• [BioC] DESeq estimateDispersions   Michael Love
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Michael Love
• [BioC] question about using exomeCopy on a single exome sample   Michael Love
• [BioC] ExomeCopy error   Michael Love
• [BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)   Jack Luo
• [BioC] faillure in ragene10stv1 in rat Gene St0.1 Affymetrix data   James W. MacDonald
• [BioC] faillure in ragene10stv1 in rat Gene St0.1 Affymetrix data   James W. MacDonald
• [BioC] known gene => gene symbol for UCSC   James W. MacDonald
• [BioC] known gene => gene symbol for UCSC   James W. MacDonald
• [BioC] Mass spectrometry data analysis   James W. MacDonald
• [BioC] Make cdf package error Human Exon array   James W. MacDonald
• [BioC] Make cdf package error Human Exon array   James W. MacDonald
• [BioC] trouble installing affycoretools for R 3.0   James W. MacDonald
• [BioC] Problem with Limma - Possible Limma/affy bug - minimal code not working   James W. MacDonald
• [BioC] Problem with Limma - Possible Limma/affy bug - minimal code not working - Solved - Minor doubt   James W. MacDonald
• [BioC] question about model.matrix and makeContrasts for limma   James W. MacDonald
• [BioC] ReportingTools error   James W. MacDonald
• [BioC] ReportingTools error   James W. MacDonald
• [BioC] How to use 'ebayes' for small samples?   James W. MacDonald
• [BioC] Microarray Analysis of Rat Gene 2.0 ST arrays   James W. MacDonald
• [BioC] nsFilter error in genefilter   James W. MacDonald
• [BioC] Limma to find differentially expressed genes   James W. MacDonald
• [BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)   James W. MacDonald
• [BioC] an error in AnnotationForge   James W. MacDonald
• [BioC] rma command error in oligo package   James W. MacDonald
• [BioC] Visualization and Interpretation of Go Terms   James W. MacDonald
• [BioC] Chip Definition File (CDF) for Affymetrix microRNA Arrays 3.0   James W. MacDonald
• [BioC] Chip Definition File (CDF) for Affymetrix microRNA Arrays 3.0   James W. MacDonald
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results   James W. MacDonald
• [BioC] Add new affy organism platform   James W. MacDonald
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy   James W. MacDonald
• [BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy   James W. MacDonald
• [BioC] Affymetrix CEL files   James W. MacDonald
• [BioC] Affymetrix CEL files   James W. MacDonald
• [BioC] RNAseq analyses: to use, or not use, all the samples; that's the question.   Aaron Mackey
• [BioC] add txt labels to points in plot from splom   Alyaa Mahmoud
• [BioC] Useful information about Ensembl release 71 mart databases   Thomas Maurel
• [BioC] fRMA for Gene ST arrays   Matthew McCall
• [BioC] Normalizing a dataset from GEO to suit a classifier trained on another dataset   Matthew McCall
• [BioC] Normalizing a dataset from GEO to suit a classifier trained on another dataset   Matthew McCall
• [BioC] rtracklayer importing gtf files   Sam McInturf
• [BioC] Affymetrix HTA 2 array analysis   Steven McKinney
• [BioC] edgeR for entirely individual gene wise dispersion   Gu Mi
• [BioC] HTqPCR package-problems creating qPCR set; format "Open Array"   Katharina Michael
• [BioC] Help with flowCore   Mike
• [BioC] [R] Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY   Martin Morgan
• [BioC] trouble installing affycoretools for R 3.0   Martin Morgan
• [BioC] how to get the CEL files of CLL package   Martin Morgan
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Martin Morgan
• [BioC] BiocInstaller on R-devel   Martin Morgan
• [BioC] BiocInstaller on R-devel   Martin Morgan
• [BioC] Error when try VariantAnnotation filterVcf vignette example   Martin Morgan
• [BioC] Help needed! What wrong with VariantAnnotation and TCGA vcfs   Martin Morgan
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Martin Morgan
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Martin Morgan
• [BioC] DESeq2   Martin Morgan
• [BioC] Using Precede in GenomicRanges   Martin Morgan
• [BioC] GO enrichment on an ordered list of genes   Martin Morgan
• [BioC] Bioc 2013 Conference in Seattle, July 18-19 -- Updates   Martin Morgan
• [BioC] transport mcols from one GRange obejct to another   Martin Morgan
• [BioC] Deleting object rows while looping   Martin Morgan
• [BioC] Problems with SVGAnnotation package   Martin Morgan
• [BioC] Deleting object rows while looping - II   Martin Morgan
• [BioC] Make cdf package error Human Exon array   Maria Arnedo Munoz
• [BioC] Interpreting DESeq2 results   Michael Muratet
• [BioC] Interpreting DESeq2 results   Michael Muratet
• [BioC] fRMA for Gene ST arrays   Naxerova, Kamila
• [BioC] snp coordinates   Hermann Norpois
• [BioC] Granges: range (gr) does not function   Hermann Norpois
• [BioC] transform gwaa.data (Genabel) to snp.matrix (chopsticks)   Hermann Norpois
• [BioC] Using Precede in GenomicRanges   Tom Oates
• [BioC] exonsBy order   Valerie Obenchain
• [BioC] definition for intergenic SNPs in locateVariants function   Valerie Obenchain
• [BioC] definition for intergenic SNPs in locateVariants function   Valerie Obenchain
• [BioC] definition for intergenic SNPs in locateVariants function   Valerie Obenchain
• [BioC] expand() vcf with no info columns   Valerie Obenchain
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Valerie Obenchain
• [BioC] Granges: range (gr) does not function   Valerie Obenchain
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Valerie Obenchain
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Valerie Obenchain
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Valerie Obenchain
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Valerie Obenchain
• [BioC] ensemblVEP: passing on coverage / frequency information   Valerie Obenchain
• [BioC] Annotated a snp list to find where these snp are located.   Valerie Obenchain
• [BioC] ensemblVEP: passing on coverage / frequency information   Valerie Obenchain
• [BioC] ensemblVEP: passing on coverage / frequency information   Valerie Obenchain
• [BioC] Subsetting vcf file by subject   Valerie Obenchain
• [BioC] writeVcf bug   Valerie Obenchain
• [BioC] Using Precede in GenomicRanges   Valerie Obenchain
• [BioC] Problem reading VCF file using readVcf from package VariantAnnotation   Valerie Obenchain
• [BioC] EBImage: remove objects on the edge of an image.   Andrzej Oleś
• [BioC] EBImage: remove objects on the edge of an image.   Andrzej Oleś
• [BioC] Error: package ŒGenomicRanges¹ 1.11.45 was found, but >= 1.11.46 is required by ŒBSgenome¹   Ou, Jianhong
• [BioC] Error: package ŒGenomicRanges¹ 1.11.45 was found, but >= 1.11.46 is required by ŒBSgenome¹   Ou, Jianhong
• [BioC] question about model.matrix and makeContrasts for limma   Ou, Jianhong
• [BioC] question about model.matrix and makeContrasts for limma   Ou, Jianhong
• [BioC] Limit on number of sequence files for forging a BSgenome   Hervé Pagès
• [BioC] Finding mismatches between reads and reference sequence   Hervé Pagès
• [BioC] GRanges() and naming of metadata columns has changed   Hervé Pagès
• [BioC] Granges: range (gr) does not function   Hervé Pagès
• [BioC] stringDist ?   Hervé Pagès
• [BioC] Deleting object rows while looping - II   Hervé Pagès
• [BioC] writeVcf bug   Richard Pearson
• [BioC] writeVcf bug   Richard Pearson
• [BioC] DESeq estimateDispersions   Lucia Peixoto
• [BioC] DESeq estimateDispersions   Lucia Peixoto
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Lucia Peixoto
• [BioC] beyond gene differential expression   Wang Peter
• [BioC] beyond gene differential expression   Wang Peter
• [BioC] how to get the CEL files of CLL package   Wang Peter
• [BioC] an error in AnnotationForge   Wang Peter
• [BioC] an error in AnnotationForge   Wang Peter
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Miles Pufall
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Pufall, Miles A
• [BioC] definition for intergenic SNPs in locateVariants function   Adaikalavan Ramasamy
• [BioC] definition for intergenic SNPs in locateVariants function   Adaikalavan Ramasamy
• [BioC] definition for intergenic SNPs in locateVariants function   Adaikalavan Ramasamy
• [BioC] definition for intergenic SNPs in locateVariants function   Adaikalavan Ramasamy
• [BioC] (no subject)   Abdul Rawoof
• [BioC] Differences between lmfit model(from limma package) and Illumina-custom Model(from GenomeStudio).   Abdul Rawoof
• [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements   Laya Rose
• [BioC] DEXSeq html report error   Natasha Sahgal
• [BioC] ensemblVEP: passing on coverage / frequency information   Thomas Sandmann
• [BioC] ensemblVEP: passing on coverage / frequency information   Thomas Sandmann
• [BioC] GEOquery not parsing GSE expression sets   Lucas Santana dos Santos
• [BioC] GEOquery not parsing GSE expression sets   Lucas Santana dos Santos
• [BioC] GEOquery not parsing GSE expression sets   Lucas Santana dos Santos
• [BioC] BHC appears to be broken   Rich Savage
• [BioC] Unexpected Results from Limma background subtraction & marray normalizatoin   Ellen Sebastian
• [BioC] Unexpected output from Limma background subtraction & Normalization   Ellen Sebastian
• [BioC] Error when try VariantAnnotation filterVcf vignette example   Paul Shannon
• [BioC] Doubt RCytoscape   Paul Shannon
• [BioC] cn.mops: copy number for low-coverage bam files?   Paul Shannon
• [BioC] cn.mops: copy number for low-coverage bam files?   Paul Shannon
• [BioC] beyond gene differential expression   Wei Shi
• [BioC] Rsubread aligner NEWS   Wei Shi
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Wei Shi
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Wei Shi
• [BioC] need help for the study design of a RNA-Seq project   Wei Shi
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Wei Shi
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Wei Shi
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Wei Shi
• [BioC] mapping multi-mapping reads in Rsubread (summarizeOverlaps mode ignoring inter feature overlaps)   Wei Shi
• [BioC] loss of stranding in alignments from recent versions of Rsubread   Wei Shi
• [BioC] Doubt RCytoscape   Ricardo Silva
• [BioC] Normalizing a dataset from GEO to suit a classifier trained on another dataset   Nathan Skene
• [BioC] logFC in GLM of egdeR   Gordon K Smyth
• [BioC] logFC in GLM of egdeR   Gordon K Smyth
• [BioC] EdgeR additive linear model, errors   Gordon K Smyth
• [BioC] EdgeR - generating appropriate design and contrast matrix : multi-factorial experiment   Gordon K Smyth
• [BioC] Limma - Result output - Error - Help   Gordon K Smyth
• [BioC] error and warning message with blocked samples with Limma   Gordon K Smyth
• [BioC] lmFit() with ExpressionSet   Gordon K Smyth
• [BioC] error and warning message with blocked samples with Limma   Gordon K Smyth
• [BioC] EdgeR- how to work PARTIALLY without replicates   Gordon K Smyth
• [BioC] edgeR : Include or exclude structural/noncoding RNA reads in the analysis   Gordon K Smyth
• [BioC] ReportingTools error   Gordon K Smyth
• [BioC] ReportingTools error   Gordon K Smyth
• [BioC] EdgeR 'average' cpm   Gordon K Smyth
• [BioC] lmFit not keeping rownames of arg object?   Gordon K Smyth
• [BioC] spline example from limma user's guide   Gordon K Smyth
• [BioC] lmFit not keeping rownames of arg object?   Gordon K Smyth
• [BioC] lmFit not keeping rownames of arg object?   Gordon K Smyth
• [BioC] Differences between lmfit model(from limma package) and Illumina-custom Model (from GenomeStudio)   Gordon K Smyth
• [BioC] Differences between lmfit model(from limma package) and Illumina-custom Model (from GenomeStudio)   Gordon K Smyth
• [BioC] Design matrix and BCV   Gordon K Smyth
• [BioC] Design matrix and BCV   Gordon K Smyth
• [BioC] edgeR for entirely individual gene wise dispersion   Gordon K Smyth
• [BioC] Unexpected output from Limma background subtraction & Normalization   Gordon K Smyth
• [BioC] edgeR: Using ratios (translational efficiencies) as input   Gordon K Smyth
• [BioC] Possible Bugs in Contrasts Design of edgeR   Gordon K Smyth
• [BioC] Possible Bugs in Contrasts Design of edgeR   Gordon K Smyth
• [BioC] FW: Join us for a two-day R workshop featuring bioinformatics with Bioconductor & seamless R/C++ integration.   Sparapani, Rodney
• [BioC] FW: Join us for a two-day R workshop featuring bioinformatics with Bioconductor & seamless R/C++ integration.   Rodney Sparapani
• [BioC] multiple threads on QuasR   Michael Stadler
• [BioC] multiple threads on QuasR   Michael Stadler
• [BioC] QuasR special case alignment   Michael Stadler
• [BioC] rhd5 reading variable-length strings   Steven
• [BioC] need help for the study design of a RNA-Seq project   Dario Strbenac
• [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements   Dario Strbenac
• [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements   Dario Strbenac
• [BioC] Mus.musculus package pdf not found   Ido Tamir
• [BioC] known gene => gene symbol for UCSC   Ido Tamir
• [BioC] exonsBy order   Ido Tamir
• [BioC] known gene => gene symbol for UCSC   Ido Tamir
• [BioC] Mus.musculus package pdf not found   Dan Tenenbaum
• [BioC] gmapR for R 3.0.0 installation problem?   Dan Tenenbaum
• [BioC] trouble installing affycoretools for R 3.0   Dan Tenenbaum
• [BioC] Bioconductor 2.12 is released   Dan Tenenbaum
• [BioC] Bug in biocLite?   Dan Tenenbaum
• [BioC] bioc package installation problem   Dan Tenenbaum
• [BioC] bioc package installation problem   Dan Tenenbaum
• [BioC] Error installing impute package   Dan Tenenbaum
• [BioC] Error installing (some) Bioconductor packages on Mac OSX under R-3.0.0?   Dan Tenenbaum
• [BioC] Error installing (some) Bioconductor packages on Mac OSX under R-3.0.0?   Dan Tenenbaum
• [BioC] PREDA package missing   Dan Tenenbaum
• [BioC] PREDA package missing   Dan Tenenbaum
• [BioC] Potential bug in package("rtracklayer") undefined symbol regcompA   Dan Tenenbaum
• [BioC] BHC appears to be broken   Dan Tenenbaum
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Dan Tenenbaum
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Dan Tenenbaum
• [BioC] BHC appears to be broken   Dan Tenenbaum
• [BioC] Problems with SVGAnnotation package   Dan Tenenbaum
• [BioC] Problems with SVGAnnotation package   Dan Tenenbaum
• [BioC] EdgeR- how to work PARTIALLY without replicates   Teresa
• [BioC] Question on unbalanced paired design   Ryan C. Thompson
• [BioC] summarizeOverlaps mode ignoring inter feature overlaps   Ryan C. Thompson
• [BioC] Potential bug in package("rtracklayer") undefined symbol regcompA   Thornton, Matthew
• [BioC] Potential bug in package("rtracklayer") undefined symbol regcompA   Thornton, Matthew
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Tim Triche, Jr.
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Tim Triche, Jr.
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Tim Triche, Jr.
• [BioC] Fwd: GO terms: Annotation for HumanMethylation450   Tim Triche, Jr.
• [BioC] MethyLumiSet object   Tim Triche, Jr.
• [BioC] MethyLumiSet object   Tim Triche, Jr.
• [BioC] loss of stranding in alignments from recent versions of Rsubread   Tim Triche, Jr.
• [BioC] Annotated a snp list to find where these snp are located.   Fabrice Tourre
• [BioC] MEDIPS error extending reads   Stephen Turner
• [BioC] MEDIPS error extending reads   Stephen Turner
• [BioC] MEDIPS error extending reads   Stephen Turner
• [BioC] MEDIPS error extending reads   Stephen Turner
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Stephen Turner
• [BioC] DESeq2 vs limma/voom: PCA completely different. How to proceed?   Stephen Turner
• [BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion   Umass
• [BioC] [Rd] R/Sweave/cairo/freetype bug fix.   Simon Urbanek
• [BioC] Problems with SVGAnnotation package   Kevin Ushey
• [BioC] How to use 'ebayes' for small samples?   Gundala Viswanath
• [BioC] BHC appears to be broken   Joseph Viviano
• [BioC] BHC appears to be broken   Joseph Viviano
• [BioC] lmFit not keeping rownames of arg object?   Leif Väremo
• [BioC] lmFit not keeping rownames of arg object?   Leif Väremo
• [BioC] lmFit not keeping rownames of arg object?   Leif Väremo
• [BioC] Chip Definition File (CDF) for Affymetrix microRNA Arrays 3.0   K. Weigelt
• [BioC] Pathview package for pathway based data integration and visualization   Luo Weijun
• [BioC] A question about the gage package   Luo Weijun
• [BioC] GO enrichment on an ordered list of genes   January Weiner
• [BioC] DESeq: computing 95% CI for negative binomial distribution ?   Yvan Wenger
• [BioC] DESeq: computing 95% CI for negative binomial distribution ?   Yvan Wenger
• [BioC] ConsensusClusterPlus updated   Matthew D. Wilkerson
• [BioC] Limma linear models   Wu, Di
• [BioC] easyRNAseq RPKM value equal to NA   Yonggan Wu
• [BioC] Postdoctoral Position at Brown Univ- Phylogenetic analysis of gene expression data   Zhijin Wu
• [BioC] trouble installing affycoretools for R 3.0   Zadeh, Jenny Drnevich
• [BioC] Biostatistician position in London   Kathi Zarnack
• [BioC] Problem with ChIPpeakAnno - assignChromosomeRegion   Zhu, Lihua (Julie)
• [BioC] REDseq_question   Zhu, Lihua (Julie)
• [BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion   Zhu, Lihua (Julie)
• [BioC] RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion   Zhu, Lihua (Julie)
• [BioC] How to best include hyperparameter optimization in MLInterfaces?   Andreas Bernthaler [guest]
• [BioC] faillure in ragene10stv1 in rat Gene St0.1 Affymetrix data   Antje Kammermeier [guest]
• [BioC] adj.P metod = \"BH\" many exact the same value   Bas ter Braak [guest]
• [BioC] topGO Fisher test error   Bruno Giotti [guest]
• [BioC] IdeogramTrack and bigWig file errors in Gviz   Dweebis [guest]
• [BioC] NAs introduced by marrayNorm after background subtraction with Limma   Ellen Sebastian [guest]
• [BioC] it is strange that I cannot get the fpkm by using easyRNASeq   Fuyan [guest]
• [BioC] Can \"virtualArray\" package be applied with created annotation package (.db)?   Kaj Chokeshai-u-saha [guest]
• [BioC] Microarray Analysis of Rat Gene 2.0 ST arrays   Kalpana G [guest]
• [BioC] problem installing GenomicFeatures   Kavita Garg [guest]
• [BioC] Make cdf package error Human Exon array   Maria [guest]
• [BioC] PREDA package missing   Maria [guest]
• [BioC] rma command error in oligo package   Maria [guest]
• [BioC] GenomicAnnotationsFromdataframe error   Maria [guest]
• [BioC] sva: how to incorporate adjusting variables   Meritxell Oliva [guest]
• [BioC] Normalizing a dataset from GEO to suit a classifier trained on another dataset   Nathan Skene [guest]
• [BioC] beadarray package   RS [guest]
• [BioC] rtracklayer importing gtf files   Sam McInturf [guest]
• [BioC] Differentially expressed genes from specific cell types from a single sample   Sandy [guest]
• [BioC] Limma to find differentially expressed genes   Sandy [guest]
• [BioC] Visualization and Interpretation of Go Terms   Sandy [guest]
• [BioC] ensemblVEP: passing on coverage / frequency information   Thomas Sandmann [guest]
• [BioC] Homoscedasticity   Tibor Pakozdi [guest]
• [BioC] Possible Bugs in Contrasts Design of edgeR   Yang Liu [guest]
• [BioC] DESeq2   Yemmy [guest]
• [BioC] goseq error messsage   Yemmy [guest]
• [BioC] nsFilter error in genefilter   Zhenya [guest]
• [BioC] sort error in GRange   emily [guest]
• [BioC] how to use MethyLumiM object in BMIQ(wateRmelon)   indranil [guest]
• [BioC] DESeq2   oyeyemi ajayi
• [BioC] How to best include hyperparameter optimization in MLInterfaces?   andreas.bernthaler at boehringer-ingelheim.com
• [BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion   DIOP M boyba
• [BioC] gmapR for R 3.0.0 installation problem?   ying chen
• [BioC] Error when try VariantAnnotation filterVcf vignette example   ying chen
• [BioC] Help needed! What wrong with VariantAnnotation and TCGA vcfs   ying chen
• [BioC] GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack   chris_utah
• [BioC] xps- not being able to load it   cstrato
• [BioC] Add new affy organism platform   cstrato
• [BioC] brief quesion on DESeq2   daniel.aguirre
• [BioC] brief quesion on DESeq2   daniel.aguirre
• [BioC] edgeR : Include or exclude structural/noncoding RNA reads in the analysis   gowtham
• [BioC] edgeR: Using ratios (translational efficiencies) as input   gowtham
• [BioC] Question about edgeR   Abdullah khamis
• [BioC] Question about edgeR   Abdullah khamis
• [BioC] FW: DESeq Design (val1 vs mean (val2, val3, val4))   maryam
• [BioC] Regarding Illumina's WG-DASL.   abdul rawoof
• [BioC] Setting up design matrix in Limma   sanjana sood
• [BioC] Question regarding cellhts2 output   maziz at tgen.org
• [BioC] Question regarding cellhts2 output   maziz at tgen.org
• [BioC] Question regarding cellhts2 output   maziz at tgen.org
• [BioC] AUTO: Pie Müller is out of the office. (returning 15.04.2013)   Pie.Mueller at unibas.ch
• [BioC] AUTO: Pie Müller is out of the office. (returning 30.04.2013)   Pie.Mueller at unibas.ch
• [BioC] bioc package installation problem   carol white
• [BioC] bioc package installation problem   carol white
• [BioC] number of sequence from readfastq   carol white
• [BioC] number of sequence from readfastq   carol white
• [BioC] rhd5 reading variable-length strings   steven wink
• [BioC] replace the ensemble annotation with UCSC knownGene track in library "GenomeGraphs"   shirley zhang
• [BioC] Replace the ensemble annotation with UCSC knownGene track in library "GenomeGraphs"   shirley zhang
• [BioC] need help for the study design of a RNA-Seq project   shirley zhang
• [BioC] need help for the study design of a RNA-Seq project   shirley zhang
• [BioC] need help for the study design of a RNA-Seq project   shirley zhang
• [BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)   shirley zhang

Last message date: Tue Apr 30 23:06:09 CEST 2013
Archived on: Tue Apr 30 23:07:08 CEST 2013

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