July 2009 Archives by author

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Starting: Wed Jul 1 00:01:14 CEST 2009
Ending: Fri Jul 31 23:01:56 CEST 2009
Messages: 521

• [BioC] why 3UTR sequences cannot be obtained any more?   michael watson (IAH-C)
• [BioC] how to merge replicate spots?   michael watson (IAH-C)
• [BioC] neverending GO problems   michael watson (IAH-C)
• [BioC] Info about GO package   michael watson (IAH-C)
• [BioC] Problems with biomaRt   michael watson (IAH-C)
• [BioC] Problems with biomaRt   michael watson (IAH-C)
• [BioC] Statistics for next-generation sequencing transcriptomics   michael watson (IAH-C)
• [BioC] Statistics for next-generation sequencing transcriptomics   michael watson (IAH-C)
• [BioC] Statistics for next-generation sequencing transcriptomics   michael watson (IAH-C)
• [BioC] Help with contrast matrix   john seers (IFR)
• [BioC] Problems with biomaRt   john seers (IFR)
• [BioC] R: Help request about GEOquery and GSE9820   Manca Marco (PATH)
• [BioC] How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] R: How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] R: How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] R: Re: Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] R: R: Re: Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE   Manca Marco (PATH)
• [BioC] Minor problem with siggenes's command sam2excel when entrez=TRUE   Manca Marco (PATH)
• [BioC] NimbleGen HG18 CGH data   Abcis
• [BioC] XstringViews and Fasta   Patrick Aboyoun
• [BioC] error installing R 2.9.1 from source on mac os 10.5?   Patrick Aboyoun
• [BioC] RefSeq summary from biomaRt   Gad Abraham
• [BioC] Statistics for next-generation sequencing transcriptomics   Cei Abreu-Goodger
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Axel.Klenk at Actelion.Com
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Axel.Klenk at Actelion.Com
• [BioC] topGO "under-represented" GO terms?   Adrian Alexa
• [BioC] how to merge replicate spots?   Naomi Altman
• [BioC] Warning serious?   Naomi Altman
• [BioC] design a modelMatrix with no common references   Naomi Altman
• [BioC] hello!   Naomi Altman
• [BioC] effect of normalization on analysis of differential knockdown   Naomi Altman
• [BioC] effect of normalization on analysis of differential knockdown   Naomi Altman
• [BioC] Fwd: edgeR with only 1 replicate?   Naomi Altman
• [BioC] Regarding hexbin in R...   Naomi Altman
• [BioC] Statistics for next-generation sequencing transcriptomics   Naomi Altman
• [BioC] Creating one matrix of intensity data from 4 diffrent CEL files   Radhika Ambatipudi
• [BioC] is there an identifier that uniquely identifies a gene all over the many databases ?   Simon Anders
• [BioC] R: is there an identifier that uniquely identifies a gene all over the many databases ?   Simon Anders
• [BioC] flowCore::parameters   Bastian Angermann
• [BioC] flowCore::parameters   Bastian Angermann
• [BioC] flowCore::parameters   Bastian Angermann
• [BioC] Question on importing large dataset (1.4GB) into R-Bioconductor   Anqi
• [BioC] Question on the paired ttest in multtest package   Anqi
• [BioC] Questions about multtest   Anqi
• [BioC] XstringViews and Fasta   Droit Arnaud
• [BioC] XstringViews and Fasta   Droit Arnaud
• [BioC] You have 1 new ALERT message   St.George Bank
• [BioC] Limma lmFit function and spot quality weights   Benoit
• [BioC] Limma lmFit function and spot quality weights   Benoit
• [BioC] question about p-values in maSigPro   Dick Beyer
• [BioC] question about p-values in maSigPro   Dick Beyer
• [BioC] Using bgAdjust.affy for lumi   Michal Blazejczyk
• [BioC] need advice with creating an eSet with a different type of phenodata   Manisha Brahmachary
• [BioC] Software to find the area of a shape in an image   Daniel Brewer
• [BioC] Question on LIMMA   Francisco Javier Burguillo
• [BioC] Error "Specified environment does not contain MoGene-1_0-st-v1"   Vincent Carey
• [BioC] Errors using particular 'Affy' package functions   Vincent Carey
• [BioC] pd.hugene.1.0.st.v1   Vincent Carey
• [BioC] Changes in annotations?   Marc Carlson
• [BioC] GO categories in R for A. Thaliana   Marc Carlson
• [BioC] GO.db query error?   Marc Carlson
• [BioC] GO.db query error?   Marc Carlson
• [BioC] What should be the output after processing a cel file?   Marc Carlson
• [BioC] Wrong package title in mogene10stprobeset.db and mogene10sttranscriptcluster.db   Marc Carlson
• [BioC] How to add annotation information?   Marc Carlson
• [BioC] How to add annotation information?   Marc Carlson
• [BioC] How to add annotation information?   Marc Carlson
• [BioC] 2 color Nimblegen data and limma   Carvalho, Benilton
• [BioC] downloading a conservation track with rtracklayer on several chromosome seqs   Robert Castelo
• [BioC] design a modelMatrix with no common references   Robert Castelo
• [BioC] design a modelMatrix with no common references   Robert Castelo
• [BioC] how to merge replicate spots?   Barbara Cegielska
• [BioC] how to normalize microarrays using external spike controls?   Barbara Cegielska
• [BioC] neverending GO problems   Barbara Cegielska
• [BioC] [Fwd: how to merge replicate spots?]   Barbara Cegielska
• [BioC] [Fwd: how to normalize microarrays using external spike controls?]   Barbara Cegielska
• [BioC] [Fwd: neverending GO problems]   Barbara Cegielska
• [BioC] how to merge replicate spots?   Barbara Cegielska
• [BioC] [Fwd: how to merge replicate spots?]   Barbara Cegielska
• [BioC] [Fwd: t-test]   Barbara Cegielska
• [BioC] [Fwd: t-test]   Barbara Cegielska
• [BioC] gene universe   Barbara Cegielska
• [BioC] gene universe   Barbara Cegielska
• [BioC] [Fwd: t-test]   Barbara Cegielska
• [BioC] spike-dependent microarray normalization   Barbara Cegielska
• [BioC] [Fwd: spike-dependent microarray normalization]   Barbara Cegielska
• [BioC] question about p-values in maSigPro   Ana Conesa
• [BioC] BiomaRt error   Aedin Culhane
• [BioC] BiomaRt error   Aedin Culhane
• [BioC] Custom CDF Version 12 is released   Manhong Dai
• [BioC] Normalization of array data from GEO repository   Sean Davis
• [BioC] Reading function for Affymetrix BAR-Files   Sean Davis
• [BioC] Question on importing large dataset (1.4GB) into R-Bioconductor   Sean Davis
• [BioC] Help request about GEOquery and GSE9820   Sean Davis
• [BioC] Question on importing large dataset (1.4GB) into R-Bioconductor   Sean Davis
• [BioC] colorscheme in heatmap.2   Sean Davis
• [BioC] averaging multiple probes for same gene on agilent array   Sean Davis
• [BioC] NimbleGen HG18 CGH data   Sean Davis
• [BioC] How to use GEOquery to extract more than the default information from a GSE   Sean Davis
• [BioC] Filtering genes in illumina datasets obtained with GEOquery   Sean Davis
• [BioC] R: Gene_Bank_Access_Number   Sean Davis
• [BioC] need advice with creating an eSet with a different type of phenodata   Sean Davis
• [BioC] Why am I finding a mismatch between refseq_dna and ensembl_transcript_id ?   Sean Davis
• [BioC] R: Why am I finding a mismatch between refseq_dna and ensembl_transcript_id ?   Sean Davis
• [BioC] Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE   Sean Davis
• [BioC] R: Re: Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE   Sean Davis
• [BioC] venn diagram   Sean Davis
• [BioC] Statistics for next-generation sequencing transcriptomics   Zeljko Debeljak
• [BioC] Statistics for next-generation sequencing transcriptomics   Zeljko Debeljak
• [BioC] codelink database submission IDs changing   Diego Diez
• [BioC] Statistics for next-generation sequencing transcriptomics   Michael Dondrup
• [BioC] Statistics for next-generation sequencing transcriptomics   Michael Dondrup
• [BioC] How to do poisson distribution test like this?   Michael Dondrup
• [BioC] Using package GenomeGraphs with genomes not in ensemble   Michael Dondrup
• [BioC] Reading GFF files into R and GenomeGraphs   Michael Dondrup
• [BioC] about the annotate the new genome for geneplotter/genegraph   Michael Dondrup
• [BioC] Fwd: edgeR with only 1 replicate?   Jenny Drnevich
• [BioC] venn diagram   Jenny Drnevich
• [BioC] Creating LumiBatch object from ExpressionSet   Pan Du
• [BioC] Creating LumiBatch object from ExpressionSet   Pan Du
• [BioC] Problem with Beadarray package for beadchipHT-12   Mark Dunning
• [BioC] bead-level data from Infinium methylation arrays   Mark Dunning
• [BioC] JOB: Cancer Research UK - Cambridge Research Institute Bioinformatics Core   Mark Dunning
• [BioC] Problem with Ringo   Heidi Dvinge
• [BioC] Bug in vsn2   "M. Gonzalo Claros Díaz"
• [BioC] Problem with Ringo   Hari Easwaran
• [BioC] Filter before? Filter after? With maanova   Loren Engrav
• [BioC] Commands with maanova   Loren Engrav
• [BioC] Changes in annotations?   Loren Engrav
• [BioC] Filter before? Filter after? With maanova   Loren Engrav
• [BioC] Changes in annotations?   Loren Engrav
• [BioC] Warning serious?   Loren Engrav
• [BioC] Warning serious?   Loren Engrav
• [BioC] What does maanova contrast?   Loren Engrav
• [BioC] Ignore maanova warning messages?   Loren Engrav
• [BioC] Changes in annotations?   Loren Engrav
• [BioC] To bioinformatics and maanova expert   Loren Engrav
• [BioC] Analysis HumanHT-12 Illumina   Stefanie Figura
• [BioC] Analysis HumanHT-12 Illumina   Stefanie Figura
• [BioC] RMA normalization issue   Fuying Gao
• [BioC] design a modelMatrix with no common references   Giusy Della Gatta
• [BioC] design a modelMatrix with no common references   Giusy Della Gatta
• [BioC] design a modelMatrix with no common references   Giusy Della Gatta
• [BioC] How to extract probe sequence and probe name info from bpmap files   Laurent Gautier
• [BioC] Software to find the area of a shape in an image   Laurent Gautier
• [BioC] Map gene expression to location in genome.   Paul Geeleher
• [BioC] Filter before? Filter after? With maanova   Robert Gentleman
• [BioC] gene universe   Robert Gentleman
• [BioC] rowQ failed   Robert Gentleman
• [BioC] problem installing Bioconductor   Robert Gentleman
• [BioC] annotation package for HPRD   Robert Gentleman
• [BioC] Venn Diagram   Thomas Girke
• [BioC] Venn Diagram   Thomas Girke
• [BioC] problem with 2.0 cdf   Alberto Goldoni
• [BioC] 07-27-09 PK Graphics Weekly!! Summer Special - 10k 4x6's for $200. Special running all week.   PK Graphics
• [BioC] flowViz xyplot smooth=F gate outline ONLY   Aric Gregson
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Edwin Groot
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Edwin Groot
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Edwin Groot
• [BioC] LIMMA: Why does eBayes expression differ from observed?   Edwin Groot
• [BioC] Error "Specified environment does notcontain MoGene-1_0-st-v1"   Groot, Philip de
• [BioC] CDF file for Affy GeneChip miRNA array   Groot, Philip de
• [BioC] [R] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?   Gabor Grothendieck
• [BioC] Clustering time-course data   Priscila Grynberg
• [BioC] some questions about RNAi hit selection   Rajarshi Guha
• [BioC] some questions about RNAi hit selection   Rajarshi Guha
• [BioC] effect of normalization on analysis of differential knockdown   Rajarshi Guha
• [BioC] A question on variance adjustment of HTS plates   Rajarshi Guha
• [BioC] annotation package for HPRD   Rajarshi Guha
• [BioC] Software to find the area of a shape in an image   Jordi Altirriba Gutiérrez
• [BioC] flowCore::parameters   Florian Hahne
• [BioC] flowCore::parameters   Florian Hahne
• [BioC] CellHTS Replicates Missing   Florian Hahne
• [BioC] An issue in flowCore-package (?)   Florian Hahne
• [BioC] PRO-NEST postdoc position PHILIPS RESEARCH. prostate cancer functional biomarker validation (www.pro-nest.com)   Paul Hammer
• [BioC] Venn Diagram   Thomas Hampton
• [BioC] Venn Diagram   Thomas Hampton
• [BioC] some questions about RNAi hit selection   Thomas Hampton
• [BioC] 2 color Nimblegen data and limma   Thomas Hampton
• [BioC] 2 color Nimblegen data and limma   Thomas Hampton
• [BioC] Rmpi over mpich on Red Hat beowolf cluster   Thomas Hampton
• [BioC] colorscheme in heatmap.2   Thomas Hampton
• [BioC] data normalization   Thomas Hampton
• [BioC] Unable to install Rgraphviz   Kasper Daniel Hansen
• [BioC] Regarding hexbin in R...   Kasper Daniel Hansen
• [BioC] Non linear intensities   Kasper Daniel Hansen
• [BioC] internal error in package Rgraphviz: "cdt.dll not found"   Kasper Daniel Hansen
• [BioC] Thanks   Harikrishnadhar
• [BioC] Statistics for next-generation sequencing transcriptomics   John Herbert
• [BioC] Software to find the area of a shape in an image   Susan Holmes
• [BioC] Limma: how to extract mean of groups?   Hooiveld, Guido
• [BioC] Limma: how to extract mean of groups?   Hooiveld, Guido
• [BioC] Limma: how to extract mean of groups?   Hooiveld, Guido
• [BioC] CDF file for Affy GeneChip miRNA array   Hooiveld, Guido
• [BioC] about the annotate the new genome for geneplotter/genegraph   zhuocheng Hou
• [BioC] Please help me with contrast matrix!!!!!!!!!!!!!   Jenny Huang
• [BioC] Help with contrast matrix   Jenny Huang
• [BioC] EMBL Interdisciplinary Postdoc Programme   Wolfgang Huber
• [BioC] EBImage installation problem on Linux   Wolfgang Huber
• [BioC] Reference Normalization using vsn2   Wolfgang Huber
• [BioC] Bug in vsn2   Wolfgang Huber
• [BioC] Analysis HumanHT-12 Illumina   Wolfgang Huber
• [BioC] A question on variance adjustment of HTS plates   Wolfgang Huber
• [BioC] effect of normalization on analysis of differential knockdown   Wolfgang Huber
• [BioC] biomaRt does not like flies   Wolfgang Huber
• [BioC] effect of normalization on analysis of differential knockdown   Wolfgang Huber
• [BioC] Scientific Programmer: Next Gen Sequencing / AYB at European Bioinformatics Institute - Cambridge, UK   Wolfgang Huber
• [BioC] Problem with Ringo   Wolfgang Huber
• [BioC] Fisher's test on my annotated categories   Wolfgang Huber
• [BioC] Group samples on heatmap?   Michael Imbeault
• [BioC] how to use writeFASTA in modality "append"   Alvaro Cuadros Inostroza
• [BioC] Urgent..........Problem in using ABarray   Priyanka Jain
• [BioC] Fwd: Urgent..........Problem in using ABarray   Priyanka Jain
• [BioC] How to do poisson distribution test like this?   Mao Jianfeng
• [BioC] Fisher's test on my annotated categories   Adrian Johnson
• [BioC] Mapping Agilent Probes   Marten Jäger
• [BioC] Donate for text link   Martin Kicko
• [BioC] biomaRt archives   Rhoda Kinsella
• [BioC] Ensembl mart issues   Rhoda Kinsella
• [BioC] Ensembl mart issues   Rhoda Kinsella
• [BioC] Ensembl mart issues   Rhoda Kinsella
• [BioC] internal error in package Rgraphviz: "cdt.dll not found"   Fatima Kreusch
• [BioC] Beadarray package   Mohamed Lajnef
• [BioC] limma or beadarray for Illumina microarray ?   Mohamed Lajnef
• [BioC] Limma: how to extract mean of groups?   Mohamed Lajnef
• [BioC] Differential expression ( Limma) for illumina microarrays?   Mohamed Lajnef
• [BioC] Differential expression ( Limma) for illumina microarrays?   Mohamed Lajnef
• [BioC] rtracklayer <-> UCSC interaction currently broken   Michael Lawrence
• [BioC] rtracklayer <-> UCSC interaction currently broken   Michael Lawrence
• [BioC] downloading a conservation track with rtracklayer on several chromosome seqs   Michael Lawrence
• [BioC] examples of "ucscTableQuery" in "rtracklayer" does not work   Michael Lawrence
• [BioC] rtrack export.wig   Michael Lawrence
• [BioC] problem about using 'rtracklayer' package to retrieve SNP chromosome position   Michael Lawrence
• [BioC] problem about using 'rtracklayer' package to retrieve SNP chromosome position   Michael Lawrence
• [BioC] Reading GFF files into R and GenomeGraphs   Michael Lawrence
• [BioC] Bioinformatics job- Brisbane, Australia   Paul Leo
• [BioC] Question about inspecting splices indexes (oneChannelGUI)   Guido Leoni
• [BioC] Question about inspecting splices indexes (oneChannelGUI)   Guido Leoni
• [BioC] Fwd: Question about inspecting splices indexes (oneChannelGUI)   Guido Leoni
• [BioC] analysis histone methylation of Arabidopsis at genome level by ChIP-Chip?   Daofeng Li
• [BioC] analysis histone methylation of Arabidopsis at genome level by ChIP-Chip?   Daofeng Li
• [BioC] error when using trackNames function in rtracklayer   LiGang
• [BioC] examples of "ucscTableQuery" in "rtracklayer" does not work   LiGang
• [BioC] examples of   LiGang
• [BioC] examples of   LiGang
• [BioC] problem about using 'rtracklayer' package to retrieve SNP chromosome position   LiGang
• [BioC] problem about using 'rtracklayer' to retrieve chromosome position of SNPs   LiGang
• [BioC] Normalization of array data from GEO repository   Steve Lianoglou
• [BioC] request   Steve Lianoglou
• [BioC] R: is there an identifier that uniquely identifies a gene all over the many databases ?   Steve Lianoglou
• [BioC] Bioconductor 2.4 is released   Steve Lianoglou
• [BioC] hello!   Steve Lianoglou
• [BioC] R: how to use writeFASTA in modality "append"   Steve Lianoglou
• [BioC] How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...   Steve Lianoglou
• [BioC] golubEsets on Windows/Vista   Gary Lipton
• [BioC] golubEsets on Windows/Vista   Gary Lipton
• [BioC] Annotation.db: how automatically call a mapping?   James W. MacDonald
• [BioC] Changes in annotations?   James W. MacDonald
• [BioC] limma or beadarray for Illumina microarray ?   James W. MacDonald
• [BioC] Limma: how to extract mean of groups?   James W. MacDonald
• [BioC] biomaRt: getting start and end locations of gene on chromosome   James W. MacDonald
• [BioC] Limma: how to extract mean of groups?   James W. MacDonald
• [BioC] Question on LIMMA   James W. MacDonald
• [BioC] Limma: how to extract mean of groups?   James W. MacDonald
• [BioC] how to create an affybatch   James W. MacDonald
• [BioC] Changes in annotations?   James W. MacDonald
• [BioC] HT HG-U133+ PM Array Plate: cdf and probe packages discrepancies   James W. MacDonald
• [BioC] design a modelMatrix with no common references   James W. MacDonald
• [BioC] Problems with biomaRt   James W. MacDonald
• [BioC] Error in summary(hyperGtest)   James W. MacDonald
• [BioC] Error in summary(hyperGtest)   James W. MacDonald
• [BioC] rtracklayer and gene symbols   James W. MacDonald
• [BioC] Creating CDF   James W. MacDonald
• [BioC] Creating CDF   James W. MacDonald
• [BioC] problem about using 'rtracklayer' package to retrieve SNP chromosome position   James W. MacDonald
• [BioC] data normalization   James W. MacDonald
• [BioC] overall p-value for multilevel factor in 2 way ANOVA   James W. MacDonald
• [BioC] limma   James W. MacDonald
• [BioC] Error "Specified environment does not contain MoGene-1_0-st-v1"   James W. MacDonald
• [BioC] Creating Custom CDF   James W. MacDonald
• [BioC] Creating Custom CDF   James W. MacDonald
• [BioC] Help with loop logic   James W. MacDonald
• [BioC] Problems with RMA in affy   James W. MacDonald
• [BioC] What should be the output after processing a cel file?   James W. MacDonald
• [BioC] What should be the output after processing a cel file?   James W. MacDonald
• [BioC] venn diagram   James W. MacDonald
• [BioC] Group samples on heatmap?   James W. MacDonald
• [BioC] Question on the paired ttest in multtest package   James W. MacDonald
• [BioC] hclustfun argument in heatmap.2 function   James W. MacDonald
• [BioC] POSTDOC in SYSTEMS GENETICS at Cancer Research UK Cambridge Research Institute   Florian Markowetz
• [BioC] Normalization of array data from GEO repository   Aleš Maver
• [BioC] Normalization of array data from GEO repository   Aleš Maver
• [BioC] Filtering genes in illumina datasets obtained with GEOquery   Aleš Maver
• [BioC] (no subject)   McGee, Monnie
• [BioC] problem installing Bioconductor   David Millis
• [BioC] problem installing Bioconductor   David Millis
• [BioC] Fwd: problems installing 'affy'   Cathrine Mitchell
• [BioC] Errors using particular 'Affy' package functions   Cathrine Mitchell
• [BioC] Problem with Beadarray package for beadchipHT-12   Perry Moerland
• [BioC] Gene location (Base pair number)   Martin Morgan
• [BioC] Gene location (Base pair number)   Martin Morgan
• [BioC] golubEsets on Windows/Vista   Martin Morgan
• [BioC] golubEsets on Windows/Vista   Martin Morgan
• [BioC] Fwd: problems installing 'affy'   Martin Morgan
• [BioC] Rmpi over mpich on Red Hat beowolf cluster   Martin Morgan
• [BioC] Bug in metaArray package   Martin Morgan
• [BioC] Problems with RMA in affy   Martin Morgan
• [BioC] arrayQualityMetrics   Martin Morgan
• [BioC] ExpressionSet created by procset method in ArrayExpress   Martin Morgan
• [BioC] ExpressionSet created by procset method in ArrayExpress   Martin Morgan
• [BioC] Illumina 610 Quad SNP chips   Dmitri Mouradov
• [BioC] Software to find the area of a shape in an image   Ludo Muller
• [BioC] model parameter estimation in RMA   Zufar Mulyukov
• [BioC] Problem with negative gene locations   Naira Naouar
• [BioC] Problem with negative gene locations   Naira Naouar
• [BioC] codelink database submission IDs changing   Matthew Neville
• [BioC] Problem with Beadarray package for beadchipHT-12   Leo Nitsche
• [BioC] limma or beadarray for Illumina microarray ?   Leo Nitsche
• [BioC] Venn Diagram   Simon Noël
• [BioC] Venn Diagram   Simon Noël
• [BioC] Venn Diagram   Simon Noël
• [BioC] Venn Diagram   Simon Noël
• [BioC] Venn Diagram   Simon Noël
• [BioC] venn diagram   Ochsner, Scott A
• [BioC] venn diagram   Ochsner, Scott A
• [BioC] Regarding hexbin in R...   Wells Oliver
• [BioC] Regarding hexbin in R...   Wells Oliver
• [BioC] Venn Diagram   Hervé Pagès
• [BioC] Venn Diagram   Hervé Pagès
• [BioC] Gene location (Base pair number)   Hervé Pagès
• [BioC] [Bioc-sig-seq] Error in assign while calling the vmatchPattern function   Hervé Pagès
• [BioC] RMA normalization issue   Hervé Pagès
• [BioC] BSGenomeForge   Hervé Pagès
• [BioC] Bsgenome Zv7 sequence data   Hervé Pagès
• [BioC] Map gene expression to location in genome.   Hervé Pagès
• [BioC] [Fwd: [Genome-announce] Note on human mitochondrial sequence in hg19]   Hervé Pagès
• [BioC] ArrayExpress and GEO datasets   Helen Parkinson
• [BioC] EBImage installation problem on Linux   Gregoire Pau
• [BioC] Agilent and Limma   Francois Pepin
• [BioC] hello   Francois Pepin
• [BioC] Fisher's test on my annotated categories   Francois Pepin
• [BioC] gcrma/rma using drosophila CEL files, VECTOR_ELT() problem   Tobias Petri
• [BioC] gcrma/rma using drosophila CEL files, VECTOR_ELT() problem   Tobias Petri
• [BioC] Job Posting: Biostatistician   Aimee Picard
• [BioC] R scripts from AffylmGUI   Marcos Pinho
• [BioC] build.mappings() from Agi4x44PreProcess is not helping me today   Massimo Pinto
• [BioC] R: Found seven 3'UTR sequences attributed to the same ensembl_gene_id   David K Pritchard
• [BioC] How to use ExpressionSet for further Analysis   Md.Mamunur Rashid
• [BioC] ExpressionSet created by procset method in ArrayExpress   Md.Mamunur Rashid
• [BioC] ExpressionSet created by procset method in ArrayExpress   Md.Mamunur Rashid
• [BioC] Creating LumiBatch object from ExpressionSet   Md.Mamunur Rashid
• [BioC] Creating LumiBatch object from ExpressionSet   Md.Mamunur Rashid
• [BioC] Creating LumiBatch object from ExpressionSet   Md.Mamunur Rashid
• [BioC] Normalization of array data from GEO repository   James F. Reid
• [BioC] How to use GEOquery to extract more than the default information from a GSE   James F. Reid
• [BioC] Filtering genes in illumina datasets obtained with GEOquery   James F. Reid
• [BioC] R: How to use GEOquery to extract more than the default information from a GSE   James F. Reid
• [BioC] CGHregions error   Daniel Rico
• [BioC] 2 color Nimblegen data and limma   Mark Robinson
• [BioC] Fwd: edgeR with only 1 replicate?   Mark Robinson
• [BioC] pd.hugene.1.0.st.v1   Mark Robinson
• [BioC] Mapping Agilent Probes   Peter Robinson
• [BioC] Agilent and Limma   Peter Robinson
• [BioC] Wrong package title in mogene10stprobeset.db and mogene10sttranscriptcluster.db   David Rossell
• [BioC] biomaRt archives   Julien Roux
• [BioC] biomaRt archives   Julien Roux
• [BioC] rtracklayer and gene symbols   Christian Ruckert
• [BioC] error installing R 2.9.1 from source on mac os 10.5?   Jesper Ryge
• [BioC] error installing R 2.9.1 from source on mac os 10.5?   Jesper Ryge
• [BioC] Changes in annotations?   Alex Sanchez
• [BioC] Changes in annotations?   Alex Sanchez
• [BioC] R scripts from AffylmGUI   Keith Satterley
• [BioC] R scripts from AffylmGUI   Keith Satterley
• [BioC] CellHTS Replicates Missing   Becky Saunders
• [BioC] Normalization of array data from GEO repository   Markus Schmidberger
• [BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays   Jack Schonbrun
• [BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays   Jack Schonbrun
• [BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays   Jack Schonbrun
• [BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays   Jack Schonbrun
• [BioC] rtrack export.wig   Vince Schulz
• [BioC] Error message when working with sam   Holger Schwender
• [BioC] Minor problem with siggenes's command sam2excel when entrez=TRUE   Holger Schwender
• [BioC] Rgraphviz node size + arrowhead size   Yaniv Semel
• [BioC] Error in summary(hyperGtest)   Fraser Sim
• [BioC] Error in summary(hyperGtest)   Fraser Sim
• [BioC] Software to find the area of a shape in an image   Oleg Sklyar
• [BioC] Gene location (Base pair number)   Tim Smith
• [BioC] Gene location (Base pair number)   Tim Smith
• [BioC] biomaRt: getting start and end locations of gene on chromosome   Tim Smith
• [BioC] GO.db query error?   Tim Smith
• [BioC] GWAS and gene expression datasets for same cases?   Tim Smith
• [BioC] Differential expression ( Limma) for illumina microarrays?   Gordon K Smyth
• [BioC] Normalization using control spots   Gordon K Smyth
• [BioC] Normalization using control spots   Gordon K Smyth
• [BioC] Limma lmFit function and spot quality weights   Gordon K Smyth
• [BioC] KEGGSOAP package: I can't retrieve KEGG pathway diagrams   Paolo Sonego
• [BioC] Warning serious?   Juan Pedro Steibel
• [BioC] 2 color Nimblegen data and limma   Tobias Straub
• [BioC] Agilent and Limma   Tobias Straub
• [BioC] averaging multiple probes for same gene on agilent array   Tobias Straub
• [BioC] necessitated   Stuhr
• [BioC] venn diagram   Stephen V. Su
• [BioC] venn diagram   Stephen V. Su
• [BioC] some questions about RNAi hit selection   Ian Sudbery
• [BioC] how to create an affybatch   Venkat Sundar
• [BioC] how to create an affybatch   Venkat Sundar
• [BioC] TP and FP   Venkat Sundar
• [BioC] Job Opportunity at IMP, Vienna, Austria   Ido M. Tamir
• [BioC] Statistics for next-generation sequencing transcriptomics   Margaret Taub
• [BioC] GO categories in R for A. Thaliana   Vishal Thapar
• [BioC] Reading function for Affymetrix BAR-Files   Philippe Thomas
• [BioC] bead-level data from Infinium methylation arrays   Tim Triche, Jr.
• [BioC] bead-level data from Infinium methylation arrays   Tim Triche, Jr.
• [BioC] Missing Autocorrelation in Ringo   Joern Toedling
• [BioC] Post-doc position in Paris   Joern Toedling
• [BioC] Normalization of array data from GEO repository   Joern Toedling
• [BioC] problem with 2.0 cdf   Joern Toedling
• [BioC] problem with 2.0 cdf   Joern Toedling
• [BioC] Advice for ChIPchip-Analysis   Joern Toedling
• [BioC] hclustfun argument in heatmap.2 function   Joern Toedling
• [BioC] Bioconductor 2.4 is released   Bob Treder
• [BioC] .idat, .locs, .sdf (+ .txt) files from Illumina Infinium beadarrays   Tim Triche
• [BioC] background correction on PM only: compute.affinities2()   Marianne Tuefferd
• [BioC] HT HG-U133+ PM Array Plate: cdf and probe packages discrepancies   Marianne Tuefferd
• [BioC] underpc   UNDERPC
• [BioC] BeadarraySNP/read.SnpSetIllumina   Boris Umylny
• [BioC] data normalization   Barbara Uszczynska
• [BioC] I did the normalization.   Barbara Uszczynska
• [BioC] question about ontoCompare() performance change   Oana VIGY
• [BioC] Beadarray package   Vallejo, Roger
• [BioC] limma   Claire Vandiedonck
• [BioC] Missing Autocorrelation in Ringo   Torsten Waldminghaus
• [BioC] Normalization using control spots   Alison Waller
• [BioC] Normalization using control spots   Alison Waller
• [BioC] averaging multiple probes for same gene on agilent array   Alison Waller
• [BioC] Normalization Between Arrays using Control Spots   Alison Waller
• [BioC] Reference Normalization using vsn2   Sam Wong
• [BioC] heatmap.2 question - plotting gene expression ordered by a vector   Yannick Wurm
• [BioC] Fwd: Re: which package can do GSEA for no model organism   Pengcheng Yang
• [BioC] Unable to install Rgraphviz   Pengcheng Yang
• [BioC] Error "Specified environment does not contain MoGene-1_0-st-v1"   Peng Yu
• [BioC] Error "Specified environment does not contain MoGene-1_0-st-v1"   Peng Yu
• [BioC] What should be the output after processing a cel file?   Peng Yu
• [BioC] What should be the output after processing a cel file?   Peng Yu
• [BioC] What should be the output after processing a cel file?   Peng Yu
• [BioC] How to add annotation information?   Peng Yu
• [BioC] How to add annotation information?   Peng Yu
• [BioC] Bsgenome Zv7 sequence data   Julie Zhu
• [BioC] Error accessing archived sequences for Zv7   Julie Zhu
• [BioC] Bsgenome Zv7 sequence data   Julie Zhu
• [BioC] Bsgenome Zv7 sequence data   Julie Zhu
• [BioC] Bsgenome Zv7 sequence data   Julie Zhu
• [BioC] Advice for ChIPchip-Analysis   Karin Zimmermann
• [BioC] Advice for ChIPchip-Analysis   Karin Zimmermann
• [BioC] R: Found seven 3'UTR sequences attributed to the same ensembl_gene_id   mauede at alice.it
• [BioC] error in getBM ... Query ERROR: caught BioMart::Exception:   mauede at alice.it
• [BioC] How can I del with the error in getBM ... Query ERROR: caught BioMart::Exception:   mauede at alice.it
• [BioC] why 3UTR sequences cannot be obtained any more?   mauede at alice.it
• [BioC] why 3UTR sequences cannot be obtained any more?   mauede at alice.it
• [BioC] I: Help with symbol names mapping between miRecords and BioMart   mauede at alice.it
• [BioC] Can I use such identifier to interrogate BioMart ?   mauede at alice.it
• [BioC] Is the miRNA Mature Accession Number recorded anyhow associated to the miRNA target-gene ?   mauede at alice.it
• [BioC] is there any database where miRNA Mature Accession Number is related to the miRNA target-gene ?   mauede at alice.it
• [BioC] is there an identifier that uniquely identifies a gene all over the many databases ?   mauede at alice.it
• [BioC] R: is there an identifier that uniquely identifies a gene all over the many databases ?   mauede at alice.it
• [BioC] how to use writeFASTA in modality "append"   mauede at alice.it
• [BioC] R: how to use writeFASTA in modality "append"   mauede at alice.it
• [BioC] R: R: how to use writeFASTA in modality "append"   mauede at alice.it
• [BioC] How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...   mauede at alice.it
• [BioC] R: How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...   mauede at alice.it
• [BioC] Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't find file:   mauede at alice.it
• [BioC] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?   mauede at alice.it
• [BioC] Gene_Bank_Access_Number   mauede at alice.it
• [BioC] R: Gene_Bank_Access_Number   mauede at alice.it
• [BioC] Why am I finding a mismatch between refseq_dna and ensembl_transcript_id ?   mauede at alice.it
• [BioC] another mismatch   mauede at alice.it
• [BioC] R: Why am I finding a mismatch between refseq_dna and ensembl_transcript_id ?   mauede at alice.it
• [BioC] bioconductor package for gene shaving   somnath bandyopadhyay
• [BioC] justRMA() using different versions of affy   cstrato
• [BioC] Related to color scheme in R   ankhee dutta
• [BioC] colorscheme in heatmap.2   ankhee dutta
• [BioC] construct chromosome map in R   ankhee dutta
• [BioC] Ensembl mart release 55: Useful information   rhoda at ebi.ac.uk
• [BioC] problem installing Bioconductor   cwon2 at fhcrc.org
• [BioC] Venn Diagram   hpages at fhcrc.org
• [BioC] how to use writeFASTA in modality "append"   hpages at fhcrc.org
• [BioC] Bsgenome Zv7 sequence data   hpages at fhcrc.org
• [BioC] Help with loop logic   elliott harrison
• [BioC] Help with loop logic   elliott harrison
• [BioC] trying to do a barchart or boxplot   carolmtz at ibt.unam.mx
• [BioC] normalize.quantiles function not recognized by R   mohamed.lajnef at inserm.fr
• [BioC] request   amrit karki
• [BioC] hello!   amrit karki
• [BioC] Creating CDF   naresh kumar
• [BioC] Creating CDF   naresh kumar
• [BioC] Creating CDF   naresh kumar
• [BioC] Creating Custom CDF   naresh kumar
• [BioC] hello!   amit mandal
• [BioC] Non linear intensities   David martin
• [BioC] Non linear intensities   David martin
• [BioC] unsubscribe or change subscription to daily badge   mondtanzmond
• [BioC] overall p-value for multilevel factor in 2 way ANOVA   bernard north
• [BioC] Un logiciel de mailing pour developper vos affaires pour bioconductor   pack-prospect.pro
• [BioC] EBImage installation problem on Linux   quantrum75
• [BioC] EBImage installation problem on Linux   quantrum75
• [BioC] Question about inspecting splices indexes   rcaloger
• [BioC] Bug in metaArray package   rcaloger
• [BioC] arrayQualityMetrics   santana sarma
• [BioC] Checking for pathway membership   anupam sinha
• [BioC] Checking for pathway membership   anupam sinha
• [BioC] (no subject)   anupam sinha
• [BioC] Problems with RMA in affy   anupam sinha
• [BioC] Problems with RMA in affy   anupam sinha
• [BioC] BiomaRt error   Steffen at stat.Berkeley.EDU
• [BioC] How to extract probe sequence and probe name info from bpmap files   zhen tao
• [BioC] topGO "under-represented" GO terms?   jiayu wen
• [BioC] hclustfun argument in heatmap.2 function   carol white
• [BioC] Le site Web de votre bien immobilier pour bioconductor   ymmoo.pro
• [BioC] rowQ failed   zrl
• [BioC] rowQ failed   zrl

Last message date: Fri Jul 31 23:01:56 CEST 2009
Archived on: Fri Jul 31 23:03:14 CEST 2009

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