August 2010 Archives by date

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Starting: Sun Aug 1 11:10:17 CEST 2010
Ending: Tue Aug 31 23:57:39 CEST 2010
Messages: 500

• [BioC] SimpeAffy: how to get/generate qcdef file?   manjary singh
• [BioC] arrayQualityMetrics and Bioconductor Case Studies   Wolfgang Huber
• [BioC] get full variance per gene from DESeq   Wolfgang Huber
• [BioC] DESeq question correlation   Wolfgang Huber
• [BioC] probe ID<-> accession number   Yisong Zhen
• [BioC] Quality control on Human Affymetrix Exon microarrays   Daniel Brewer
• [BioC] best match for illumina human WG-1 vs human WG-2?   Vincent Carey
• [BioC] probe ID<-> accession number   James W. MacDonald
• [BioC] Human Affymetrix Exon microarrays   Jinyan Huang
• [BioC] Human Affymetrix Exon microarrays   Bhatti, Gaurav
• [BioC] Human Affymetrix Exon microarrays   Heidi Dvinge
• [BioC] Odd Plotting Behavior with lymphGate flowStats   Nishant Gopalakrishnan
• [BioC] best match for illumina human WG-1 vs human WG-2?   Wei Shi
• [BioC] Human Affymetrix Exon microarrays   Tim Yates
• [BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database   Samantha England
• [BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database   Georg Otto
• [BioC] How to do GO enrichment analysis with GOstats while the gene set with no p values of gene difference expression   zhidong yuan
• [BioC] xps: RMA background plot using ROOT graphics   Daniel Brewer
• [BioC] launch of free R/Bioconductor Cloud Computing web-service   hbolouri at caltech.edu
• [BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database   Marc Carlson
• [BioC] Bioconductor Digest, Vol 90, Issue 1   Amos Folarin
• [BioC] xps: RMA background plot using ROOT graphics   cstrato
• [BioC] Quality control on Human Affymetrix Exon microarrays   Wolfgang Huber
• [BioC] Fisher-test   Noe Andor
• [BioC] biomaRt problem   Wolfgang Huber
• [BioC] browseURL   Wolfgang Huber
• [BioC] fisher-test   Noemi Andor
• [BioC] arrayQualityMetrics and Bioconductor Case Studies   Chintanu
• [BioC] Statistical Bioinformatician/Geneticist Position at Oxford, UK   Stephen Taylor
• [BioC] Quality control on Human Affymetrix Exon microarrays   Daniel Brewer
• [BioC] Panels in splom (lattice) and 'class' identification   Gosink, John
• [BioC] HapMap gene list   noxyport at gmail.com
• [BioC] flowStats Plot quadrantGate Filter Result Smooth=FALSE   Chao-Jen Wong
• [BioC] HapMap gene list   Kasper Daniel Hansen
• [BioC] [R] error with ReadAffy()   James W. MacDonald
• [BioC] HapMap gene list   noxyport at gmail.com
• [BioC] Illumina GoldenGate methylation array, methylumi   Jinyan Huang
• [BioC] EBImage not loading   Henrik Failmezger
• [BioC] HapMap gene list   James W. MacDonald
• [BioC] Analysis: two-color, time series   Olga K. Kamneva
• [BioC] EBImage not loading   Gregoire Pau
• [BioC] get full variance per gene from DESeq   Graham Thomas
• [BioC] count number of groups containing consecutive numbers   ALok
• [BioC] count number of groups containing consecutive numbers   Michael Lawrence
• [BioC] clarification on MULTI SPECIES COMPARISONS filters   jorge zamora
• [BioC] ChIPpeakAnno:write2FASTA, getAllPeakSequence Functions   Zhu, Julie
• [BioC] loading processed data into eset class   Zhe Liu
• [BioC] using smoothX in Ringo   Elizabeth Ashley
• [BioC] loading processed data into eset class   Alex Gutteridge
• [BioC] loading processed data into eset class   Vincent Carey
• [BioC] loading processed data into eset class   Zhe Liu
• [BioC] [R] error with ReadAffy()   Amos Folarin
• [BioC] loading processed data into eset class   Kasper Daniel Hansen
• [BioC] loading processed data into eset class   zhliu.tju
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   Glazko, Galina
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   Peter Bazeley
• [BioC] dynamic range/scale using exprs (Biobase)   Lucia Peixoto
• [BioC] Analysis: two-color, time series   Gordon K Smyth
• [BioC] dynamic range/scale using exprs (Biobase)   Laurent Gautier
• [BioC] EBImage not loading   Henrik Failmezger
• [BioC] using smoothX in Ringo   Joern Toedling
• [BioC] browseURL   Cristobal Fresno Rodríguez
• [BioC] iFlow error in opening FCS and LMD files   Anna Dvorkin
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Karl Brand
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   James W. MacDonald
• [BioC] entrez gene to genome coordinates   Bhatti, Gaurav
• [BioC] entrez gene to genome coordinates   Marc Carlson
• [BioC] Bioconductor Developer Meeting Europe - 17.-18. 11. 2010   Wolfgang Huber
• [BioC] 'plgem' package bug fix   Pavelka, Norman
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   James W. MacDonald
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   Glazko, Galina
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   James W. MacDonald
• [BioC] Fisher-test   Naomi Altman
• [BioC] get full variance per gene from DESeq   Wolfgang Huber
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Karl Brand
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Heidi Dvinge
• [BioC] limma, is there a limited number of levels for a factor?   steve shen
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Amos Folarin
• [BioC] package for pathway analysis   Dawn
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Karl Brand
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Karl Brand
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Heidi Dvinge
• [BioC] Problem with lmfit   David martin
• [BioC] Problem with lmfit   Paolo Innocenti
• [BioC] heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)   Karl Brand
• [BioC] Problem with lmfit   David martin
• [BioC] ChIPpeakAnno - VennDiagram P-value - NaN   Zhu, Julie
• [BioC] genenames in KEGG2heatmap, GO2heatmap   Dave Bridges
• [BioC] Ensembl marts updated to rel. 59 in BioMart Central Portal   jorge zamora
• [BioC] genenames in KEGG2heatmap, GO2heatmap   James W. MacDonald
• [BioC] [limma] Separate Channel Analysis of 2 color data with summarization   Ana Conesa
• [BioC] package for pathway analysis   Richard Friedman
• [BioC] limma, is there a limited number of levels for a factor?   James W. MacDonald
• [BioC] iFlow error in opening FCS and LMD files   Josef Spidlen
• [BioC] genenames in KEGG2heatmap, GO2heatmap   James W. MacDonald
• [BioC] oligo - copying V1Overview vigenette   Lavinia Gordon
• [BioC] oligo - copying V1Overview vigenette   Benilton Carvalho
• [BioC] Problem with bnlearn and Rgraphviz   hcong at cs.usm.my
• [BioC] append on DNAStringSet produces an empty DNAString as last element   Philip Kensche
• [BioC] ChIPpeakAnno results   Marc Noguera
• [BioC] error in makeTranscriptDbFromUCSC of library(GenomicFeatures)   Yuan Jian
• [BioC] Problem with bnlearn and Rgraphviz   Martin Morgan
• [BioC] append on DNAStringSet produces an empty DNAString as last element   Martin Morgan
• [BioC] ChIPpeakAnno results   James W. MacDonald
• [BioC] Another limma factorial that needs controlling and pairing   sabrina
• [BioC] ChIPpeakAnno results   Marc Noguera
• [BioC] package for pathway analysis   Wolfgang Huber
• [BioC] Bacterial genomics   Mathieu Parent
• [BioC] SPIA with Mouse Data   Will Bush
• [BioC] package for pathway analysis   Marc Carlson
• [BioC] package for pathway analysis   mkbehnke at gmail.com
• [BioC] Bacterial genomics   Errol Strain
• [BioC] error with getMeasureRepAgreement()   Ning
• [BioC] ChIPpeakAnno results   James W. MacDonald
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   Alexandre Kuhn
• [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A   Glazko, Galina
• [BioC] Problem with lmfit   Gordon K Smyth
• [BioC] [limma] Separate Channel Analysis of 2 color data with summarization   Gordon K Smyth
• [BioC] append on DNAStringSet produces an empty DNAString as last element   Philip Kensche
• [BioC] topGO documentation / clarification   Mike Dewar
• [BioC] Another limma factorial that needs controlling and pairing   Karl Brand
• [BioC] ChIPpeakAnno results   Marc Noguera
• [BioC] Affy ST 1.0 gene chip background probes cut off set up   Stacy_Xu at bd.com
• [BioC] ArrayQualityMetrics: Grey boxes in boxplot   jeremy wilson
• [BioC] Affy ST 1.0 gene chip background probes cut off set up   James W. MacDonald
• [BioC] append on DNAStringSet produces an empty DNAString as last element   Hervé Pagès
• [BioC] Bacterial genomics   Hervé Pagès
• [BioC] TranscriptDb and genomicranges questions   Hervé Pagès
• [BioC] Affy ST 1.0 gene chip background probes cut off set up   cstrato
• [BioC] topGO documentation / clarification   Adrian Alexa
• [BioC] Long Time Series analysis   Xiaokuan Wei
• [BioC] ArrayQualityMetrics: Grey boxes in boxplot   Audrey Kauffmann
• [BioC] KEGG orthology linking (K numbers )?   Fabian Grammes
• [BioC] KEGG orthology linking (K numbers )?   Vincent Carey
• [BioC] 'Rsamtools' produces segfaults with XS tag   Andrew Tikhonov
• [BioC] How to normalize one additional CEL file?   Wiktor Mazin
• [BioC] unsupport table in GenomicFeatures   Yuan Jian
• [BioC] error with getMeasureRepAgreement()   Wolfgang Huber
• [BioC] How to normalize one additional CEL file?   Wiktor Mazin
• [BioC] How to normalize one additional CEL file?   Christian Ruckert
• [BioC] Help to confirm Design matrix and Between array Normalization.   Veerendra GP
• [BioC] How to normalize one additional CEL file?   Vincent Carey
• [BioC] mypeaklist in ChIPpeakAnno   Zhu, Julie
• [BioC] Illumina GoldenGate methylation array, methylumi   Davis, Wade
• [BioC] ArrayQualityMetrics: Grey boxes in boxplot   jeremy wilson
• [BioC] TranscriptDb and genomicranges questions   Hervé Pagès
• [BioC] KEGG orthology linking (K numbers )?   Marc Carlson
• [BioC] IRanges glitch: error restoring saved RangedData object   Michael Dondrup
• [BioC] The issue with Report Pearson instead of Spearman   Ning
• [BioC] annotation   Marcelo Brandão
• [BioC] About the AMS value in MEDME.   Jinyan Huang
• [BioC] unsupport table in GenomicFeatures   Marc Carlson
• [BioC] 'Rsamtools' produces segfaults with XS tag   Misha Kapushesky
• [BioC] annotation   Benilton Carvalho
• [BioC] Advise on setting up a non-specific filter for differential expression   Lucia Peixoto
• [BioC] limma, contrasts, and NA's   Albyn Jones
• [BioC] 'Rsamtools' produces segfaults with XS tag   Martin Morgan
• [BioC] error when loading galgo package   Qian Liu
• [BioC] error when loading galgo package   Martin Morgan
• [BioC] Normalization of polyA RNA-seq?   Xiaohui Wu
• [BioC] 'Rsamtools' produces segfaults with XS tag   Misha Kapushesky
• [BioC] 'Rsamtools' produces segfaults with XS tag   Martin Morgan
• [BioC] IRanges glitch: error restoring saved RangedData object   Martin Morgan
• [BioC] 'Rsamtools' produces segfaults with XS tag   Misha Kapushesky
• [BioC] Help to confirm Design matrix and Between array Normalization   Gordon K Smyth
• [BioC] Normalization of polyA RNA-seq?   Simon Anders
• [BioC] Normalization of polyA RNA-seq?   Ann Loraine
• [BioC] Normalization of polyA RNA-seq?   Xiaohui Wu
• [BioC] how does limma calculate the coefficients with using different design matrix?   Xiaokuan Wei
• [BioC] annotation   Marcelo Brandão
• [BioC] annotation   Benilton Carvalho
• [BioC] how does limma calculate the coefficients with using different design matrix?   Gordon K Smyth
• [BioC] how does limma calculate the coefficients with using different design matrix?   Albyn Jones
• [BioC] Affy ST 1.0 gene chip background probes cut off set up   Stacy_Xu at bd.com
• [BioC] Affy ST 1.0 gene chip background probes cut off set up   Stacy_Xu at bd.com
• [BioC] Advise on setting up a non-specific filter for differential expression   Tobias Straub
• [BioC] Another limma factorial that needs controlling and pairing   Sabrina AT Case
• [BioC] annotation   Marcelo Brandão
• [BioC] mypeaklist in ChIPpeakAnno   Zhu, Julie
• [BioC] Advise on setting up a non-specific filter for differential expression   Lucia Peixoto
• [BioC] how does limma calculate the coefficients with using different design matrix?   Xiaokuan Wei
• [BioC] Another limma factorial that needs controlling and pairing   Karl Brand
• [BioC] BioConductor and caBIG   mcoyne at boninc.com
• [BioC] how does limma calculate the coefficients with using different design matrix?   Xiaokuan Wei
• [BioC] Problems Installing EBImage on Windows XP   vwalter at email.unc.edu
• [BioC] BioConductor and caBIG   Martin Morgan
• [BioC] unmapped keys in hugene10stprobeset.db   Paul Shannon
• [BioC] unmapped keys in hugene10stprobeset.db   Marc Carlson
• [BioC] how does limma calculate the coefficients with using different design matrix?   Gordon K Smyth
• [BioC] unmapped keys in hugene10stprobeset.db   Mark Cowley
• [BioC] genArise   mcarvajal at ifc.unam.mx
• [BioC] how does limma calculate the coefficients with using different design matrix?   Xiaokuan Wei
• [BioC] genArise   Martin Morgan
• [BioC] Problems Installing EBImage on Windows XP   Martin Morgan
• [BioC] limma, contrasts, and NA's   Gordon K Smyth
• [BioC] How to normalize one additional CEL file?   Wiktor Mazin
• [BioC] flowCore read.FCS unable to read FlowJo demo data set   Johannes Rainer
• [BioC] Advise on setting up a non-specific filter for differential expression   Wolfgang Huber
• [BioC] Advise on setting up a non-specific filter for differential expression   Tobias Straub
• [BioC] The issue with Report Pearson instead of Spearman   Wolfgang Huber
• [BioC] Advise on setting up a non-specific filter for differential expression   Tobias Straub
• [BioC] Error mapping RNA-seq data to genome   Paul Geeleher
• [BioC] Advise on setting up a non-specific filter for differential expression   Lucia Peixoto
• [BioC] Error opening pdf files generated using PDF graphic device   Hari Easwaran
• [BioC] Error opening pdf files generated using PDF graphic device   Vincent Carey
• [BioC] Error opening pdf files generated using PDF graphic device   Kasper Daniel Hansen
• [BioC] Error opening pdf files generated using PDF graphic device   James W. MacDonald
• [BioC] Error opening pdf files generated using PDF graphic device   Heidi Dvinge
• [BioC] unmapped keys in hugene10stprobeset.db   Marc Carlson
• [BioC] Different result from gcrma function by using command line gcrma, affylmGUI and oneChannelGUI.   Lin Ying
• [BioC] The issue with Report Pearson instead of Spearman   Ning
• [BioC] iFlow error in opening FCS and LMD files   Anna Dvorkin
• [BioC] iFlow error in opening FCS and LMD files   Josef Spidlen
• [BioC] How to normalize one additional CEL file?   Richard Friedman
• [BioC] Error in package goseq   Joydeep Mitra
• [BioC] flowCore read.FCS unable to read FlowJo demo data set   Nishant Gopalakrishnan
• [BioC] iFlow error in opening FCS and LMD files   Wolfgang Huber
• [BioC] The issue with Report Pearson instead of Spearman   Wolfgang Huber
• [BioC] average difference and global scaling for normalizing affymetrix expression data?   Alice Johnstone
• [BioC] unmapped keys in hugene10stprobeset.db   Mark Cowley
• [BioC] get position information for different gene/transcript IDs   shirley zhang
• [BioC] flowCore read.FCS unable to read FlowJo demo data set   Johannes Rainer
• [BioC] average difference and global scaling for normalizing affymetrix expression data?   Wolfgang Huber
• [BioC] Long Time Series analysis   Maciej Jończyk
• [BioC] How to affect a color to a given label in a heatmap   sidahmed BENABDERRAHMANE
• [BioC] pa.calls-function in package "panp"   Samuel Wuest
• [BioC] labeling affy histogram   Andrew Einhorn
• [BioC] Error mapping RNA-seq data to genome   Martin Morgan
• [BioC] labeling affy histogram   James W. MacDonald
• [BioC] using smoothX in Ringo   Elizabeth Ashley
• [BioC] mypeaklist in ChIPpeakAnno   Zhu, Julie
• [BioC] using smoothX in Ringo   Joern Toedling
• [BioC] get position information for different gene/transcript IDs   Marc Carlson
• [BioC] R Courses***September - October 2010 schedule by XLSolutions Corp   Sue Turner
• [BioC] Long Time Series analysis   Xiaokuan Wei
• [BioC] Help on experiment design   Marcelo Brandão
• [BioC] get position information for different gene/transcript IDs   shirley zhang
• [BioC] Help on experiment design   Mark Cowley
• [BioC] How to affect a color to a given label in a heatmap   Mark Cowley
• [BioC] Reading image file from ImaGene 9.0   Gordon K Smyth
• [BioC] boxplot labels vertical?   Andrew Einhorn
• [BioC] boxplot labels vertical?   Cei Abreu-Goodger
• [BioC] Bioconductor-EBImage problem   Xiushan Yin
• [BioC] Help on experiment design   Marcelo Brandão
• [BioC] Creating a custom chromLocation object for cPlot   Michael Muratet
• [BioC] Using ChromHeatMap with the org.Mm.eg library   Michael Muratet
• [BioC] how to build a new bioconductor software package   wxu
• [BioC] how to build a new bioconductor software package   Steve Lianoglou
• [BioC] how to build a new bioconductor software package   wxu
• [BioC] Bioconductor-EBImage problem   Wolfgang Huber
• [BioC] get position information for different gene/transcript IDs   Marc Carlson
• [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2   Karl Brand
• [BioC] Using ChromHeatMap with the org.Mm.eg library   Marc Carlson
• [BioC] Using ChromHeatMap with the org.Mm.eg library   Tim Rayner
• [BioC] Circular binary segmentation for allele-specific CN data   Christine Ho
• [BioC] iFlow error in opening FCS and LMD files   Anna Dvorkin
• [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2   Kevin Coombes
• [BioC] Fastest way to read CSV files   Gaston Fiore
• [BioC] Fastest way to read CSV files   Sean Davis
• [BioC] Fastest way to read CSV files   Paul Leo
• [BioC] Fastest way to read CSV files   Stijn van Dongen
• [BioC] Fastest way to read CSV files   Sean Davis
• [BioC] Help on experiment design   Mark Cowley
• [BioC] Fastest way to read CSV files   Misha Kapushesky
• [BioC] Fastest way to read CSV files   Sean Davis
• [BioC] R/biomaRt problem   will.eagle at gmx.net
• [BioC] R/biomaRt problem   James W. MacDonald
• [BioC] Fastest way to read CSV files   Stijn van Dongen
• [BioC] Fastest way to read CSV files   Stijn van Dongen
• [BioC] Fastest way to read CSV files   Martin Morgan
• [BioC] Fastest way to read CSV files   Misha Kapushesky
• [BioC] xps: root.profile on a asubset of the data   Daniel Brewer
• [BioC] xps: root.profile on a asubset of the data   cstrato
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Marco Ortiz
• [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2   Karl Brand
• [BioC] xps: root.profile on a asubset of the data   Daniel Brewer
• [BioC] IRanges::Rle and missing values   Kasper Daniel Hansen
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Martin Morgan
• [BioC] IRanges::Rle and missing values   Patrick Aboyoun
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Steve Lianoglou
• [BioC] Circular binary segmentation for allele-specific CN data   Kasper Daniel Hansen
• [BioC] xps: root.profile on a asubset of the data   cstrato
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Marco Ortiz
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Martin Morgan
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Marco Ortiz
• [BioC] biomaRt and hapmap "virtualSchema" parameter mis-specification   Andrew McDavid
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Martin Morgan
• [BioC] biomaRt and hapmap "virtualSchema" parameter mis-specification   Steffen Durinck
• [BioC] Error: cannot allocate vector of size 649.8 Mb   Martin Morgan
• [BioC] Bioconductor-EBImage problem   Xiushan Yin
• [BioC] IRanges: interaction with model fitting   Kasper Daniel Hansen
• [BioC] IRanges::Rle and missing values   Patrick Aboyoun
• [BioC] IRanges: interaction with model fitting   Martin Morgan
• [BioC] Limma -time course - no replicates   Yair Benita
• [BioC] IRanges::Rle and missing values   Kasper Daniel Hansen
• [BioC] IRanges: interaction with model fitting   Kasper Daniel Hansen
• [BioC] Difficulties updating Biostrings on Ubuntu   Erik Wright
• [BioC] Difficulties updating Biostrings on Ubuntu   Benilton Carvalho
• [BioC] IRanges: interaction with model fitting   Michael Lawrence
• [BioC] gene2pathway retrain: which model is more complete?   Bogdan
• [BioC] Difficulties updating Biostrings on Ubuntu   Erik Wright
• [BioC] xps: root.profile on a asubset of the data   cstrato
• [BioC] IRanges: interaction with model fitting   Michael Lawrence
• [BioC] IRanges: interaction with model fitting   Martin Morgan
• [BioC] IRanges: interaction with model fitting   Michael Lawrence
• [BioC] Advice on a linkage program   Paul Leo
• [BioC] IRanges::Rle and missing values   Patrick Aboyoun
• [BioC] Circular binary segmentation for allele-specific CN data   J.Oosting at lumc.nl
• [BioC] Circular binary segmentation for allele-specific CN data   Christine Ho
• [BioC] xps: root.profile on a asubset of the data   Daniel Brewer
• [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2   E. McClellan
• [BioC] Error mapping RNA-seq data to genome   Paul Geeleher
• [BioC] gene2pathway retrain: which model is more complete?   Bogdan
• [BioC] Fst - sequence data   blue jay
• [BioC] Error mapping RNA-seq data to genome   Joern Toedling
• [BioC] IRanges::Rle and missing values   Kasper Daniel Hansen
• [BioC] IRanges: interaction with model fitting   Kasper Daniel Hansen
• [BioC] gene2pathway retrain: which model is more complete?   Bogdan
• [BioC] Error mapping RNA-seq data to genome   Paul Geeleher
• [BioC] Advice on a linkage program   Sean Davis
• [BioC] xps: root.profile on a asubset of the data   cstrato
• [BioC] Help on experiment design   Marcelo Brandão
• [BioC] Help on experiment design   Marc Carlson
• [BioC] gene2pathway retrain: which model is more complete?   Bogdan
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Weibo Xie
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Moshe Olshansky
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Weibo Xie
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Moshe Olshansky
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Weibo Xie
• [BioC] downloading different kinds of microarray data   Alex Levitchi
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Naomi Altman
• [BioC] downloading different kinds of microarray data   Sean Davis
• [BioC] ChIPpeakAnno, building annotations   Marc Noguera
• [BioC] downloading different kinds of microarray data   Alex Levitchi
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Steve Lianoglou
• [BioC] ChIPpeakAnno, building annotations   Hans-Rudolf Hotz
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Martin Morgan
• [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?   Weibo Xie
• [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2   Karl Brand
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Steve Lianoglou
• [BioC] Differential expresson in more than 2 samples using NGS?   Xiaohui Wu
• [BioC] downloading different kinds of microarray data   Sean Davis
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Shi, Tao
• [BioC] Two Channel miRNA exiqon data   ashwin Vishnuvardhana
• [BioC] Differential expresson in more than 2 samples using NGS?   Martin Morgan
• [BioC] Differential expresson in more than 2 samples using NGS?   Xiaohui Wu
• [BioC] xps: root.profile on a asubset of the data   cstrato
• [BioC] endoapply over GRangesList fails when an empty GRanges object is returned (Bug?)   Steve Lianoglou
• [BioC] error in RG.MA in limma   ashwin Vishnuvardhana
• [BioC] endoapply over GRangesList fails when an empty GRanges object is returned (Bug?)   Michael Lawrence
• [BioC] A code kata: evening-out *Ranges ends.   Steve Lianoglou
• [BioC] How to get position for each gene ID/gene symbol instead of position for each transcript   shirley zhang
• [BioC] A code kata: evening-out *Ranges ends.   Steve Lianoglou
• [BioC] How to get position for each gene ID/gene symbol instead of position for each transcript   Steve Lianoglou
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Steve Lianoglou
• [BioC] How to get position for each gene ID/gene symbol instead of position for each transcript   Steve Lianoglou
• [BioC] How to get position for each gene ID/gene symbol instead of position for each transcript   shirley zhang
• [BioC] A code kata: evening-out *Ranges ends.   mtmorgan at fhcrc.org
• [BioC] endoapply over GRangesList fails when an empty GRanges object is returned (Bug?)   Patrick Aboyoun
• [BioC] A code kata: evening-out *Ranges ends.   Patrick Aboyoun
• [BioC] Biobase: How to replace the ExpressionSet phenoData?   Daniel Brewer
• [BioC] Biobase: How to replace the ExpressionSet phenoData?   Daniel Brewer
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Michael Lawrence
• [BioC] A code kata: evening-out *Ranges ends.   Steve Lianoglou
• [BioC] A code kata: evening-out *Ranges ends.   Michael Lawrence
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Steve Lianoglou
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Pan Du
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Shi, Tao
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Pan Du
• [BioC] Differential expresson in more than 2 samples using NGS?   Krys Kelly
• [BioC] annotation for new agilent arrays   axel.klenk at actelion.com
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   weiliang Qiu
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Pan Du
• [BioC] Differential expresson in more than 2 samples using NGS?   Xiaohui Wu
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   weiliang Qiu
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Patrick Aboyoun
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Michael Lawrence
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Steve Lianoglou
• [BioC] Agi4x44PreProcess- RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)   Brown, Joseph
• [BioC] Agi4x44PreProcess- RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)   Benilton Carvalho
• [BioC] annotation for new agilent arrays   Marc Carlson
• [BioC] pa.calls-function in package "panp"   Fong Chun Chan
• [BioC] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?   Michael Lawrence
• [BioC] annotation for new agilent arrays   Francois Pepin
• [BioC] Differential expresson in more than 2 samples using NGS?   Gordon K Smyth
• [BioC] Differential expresson in more than 2 samples using NGS?   Gordon K Smyth
• [BioC] Differential expresson in more than 2 samples using NGS?   Xiaohui Wu
• [BioC] Scan not respecting what   Gaston Fiore
• [BioC] Scan not respecting what   Steve Lianoglou
• [BioC] Scan not respecting what   Martin Morgan
• [BioC] Scan not respecting what   Martin Morgan
• [BioC] about normalizeMethyLumiSet   gregory voisin
• [BioC] Differential expresson in more than 2 samples using NGS?   Xiaohui Wu
• [BioC] post-hoc test after F-test in Limma   Christina Orsmark-Pietras
• [BioC] using smoothX in Ringo   Elizabeth Ashley
• [BioC] annotation for new agilent arrays   Marc Carlson
• [BioC] question regarding MAS5 normalization with reduced probes   James Anderson
• [BioC] Scan not respecting what   Gaston Fiore
• [BioC] Scan not respecting what   Martin Morgan
• [BioC] Scan not respecting what   James W. MacDonald
• [BioC] Parallel Computing of varSelRF and tuneRF   Min Wang
• [BioC] Parallel Computing of varSelRF and tuneRF   Sean Davis
• [BioC] Scan not respecting what   Kasper Daniel Hansen
• [BioC] Parallel Computing of varSelRF and tuneRF   Sean Davis
• [BioC] 2do Congreso Argentino de Bioinformatica y Biologia Computacional - Cordoba 2011   Elmer Fernández
• [BioC] the order of the column name in heatmap   xiangxue Guo
• [BioC] the order of the column name in heatmap   Steve Lianoglou
• [BioC] the order of the column name in heatmap   Xianghui Liu
• [BioC] Subscripting GenomicRanges objects with [[ or $   Tim Yates
• [BioC] annotation for new agilent arrays   axel.klenk at actelion.com
• [BioC] Subscripting GenomicRanges objects with [[ or $   Richard Pearson
• [BioC] Subscripting GenomicRanges objects with [[ or $   Tim Yates
• [BioC] post-hoc test after F-test in Limma   Naomi Altman
• [BioC] Can't normalize 300+ HuGene arrays in xps   Mike Walter
• [BioC] Genominator problem   Johnny H
• [BioC] Genominator problem   Kasper Daniel Hansen
• [BioC] post-hoc test after F-test in Limma   James W. MacDonald
• [BioC] Subscripting GenomicRanges objects with [[ or $   Martin Morgan
• [BioC] Genominator problem   Johnny H
• [BioC] question regarding MAS5 normalization with reduced probes   James W. MacDonald
• [BioC] Subscripting GenomicRanges objects with [[ or $   Tim Yates
• [BioC] Genominator problem   Kasper Daniel Hansen
• [BioC] Fwd: Genominator problem   Johnny H
• [BioC] Can't normalize 300+ HuGene arrays in xps   cstrato
• [BioC] how to find probes' names in probeset   Glazko, Galina
• [BioC] Subscripting GenomicRanges objects with [[ or $   Michael Lawrence
• [BioC] Subscripting GenomicRanges objects with [[ or $   Steve Lianoglou
• [BioC] Can't normalize 300+ HuGene arrays in xps   Susan R. Atlas
• [BioC] pa.calls-function in package "panp"   Samuel Wuest
• [BioC] Can't normalize 300+ HuGene arrays in xps   cstrato
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Tim Triche
• [BioC] Limma script - Opinions requested   Orfe, Lisa
• [BioC] E. coli annotation to map?   Rayna
• [BioC] E. coli annotation to map?   Steffen Durinck
• [BioC] Can't normalize 300+ HuGene arrays in xps   cstrato
• [BioC] E. coli annotation to map?   Rayna
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Pan Du
• [BioC] Heatmap with 7120x500 array   Gaston Fiore
• [BioC] how to find probes' names in probeset   James W. MacDonald
• [BioC] illumina Infinium HumanMethylation27 detection-p-value   Tim Triche, Jr.
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Hervé Pagès
• [BioC] Involve tag count information in coverage function (IRanges, chipseq package)?   Xiaohui Wu
• [BioC] Involve tag count information in coverage function (IRanges, chipseq package)?   Xiaohui Wu
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Steve Lianoglou
• [BioC] AgiMicroRna and readMicroRnaFE   Paulo Nuin
• [BioC] Heatmap with 7120x500 array   Gerhard Thallinger
• [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?   Hervé Pagès
• [BioC] Heatmap with 7120x500 array   Martin Morgan
• [BioC] annotations of Human Gene 1.0 ST microarray and oneChannelGUI   ifig319 at ifi.csic.es
• [BioC] Limma script - Opinions requested   Gordon K Smyth
• [BioC] Limma script - Opinions requested   Gordon K Smyth
• [BioC] Advise on analyzing NGS of many genes or intergenic peaks in many conditions   Xiaohui Wu
• [BioC] help on lowess and density plot.   Veerendra GP
• [BioC] Heatmap with 7120x500 array   Paul Leo
• [BioC] normalising with bad slides   Andrew Einhorn
• [BioC] Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'   Kristel van Eijk
• [BioC] Parallel Computing of varSelRF and tuneRF   Ramon Diaz-Uriarte
• [BioC] Can I use Bioconductor to parse *.chp (Affymetrix) files?   Anton Kratz
• [BioC] Can't normalize 300+ HuGene arrays in xps   Mike Walter
• [BioC] to know about the reason in results obtained using DESeq and cufflinks   Aniket Vatsya
• [BioC] help on lowess and density plot.   James W. MacDonald
• [BioC] normalising with bad slides   James W. MacDonald
• [BioC] to know about the reason in results obtained using DESeq and cufflinks   Simon Anders
• [BioC] AgiMicroRna and readMicroRnaFE   Richard Friedman
• [BioC] DESeq and length bias [was: to know about the reason in results obtained using DESeq and cufflinks]   Simon Anders
• [BioC] question regarding MAS5 normalization with reduced probes   James Anderson
• [BioC] superimpose lowess on smoothScatter   Andrew Einhorn
• [BioC] superimpose lowess on smoothScatter   Anderson, S. Keith
• [BioC] superimpose lowess on smoothScatter   Kasper Daniel Hansen
• [BioC] question regarding MAS5 normalization with reduced probes   James W. MacDonald
• [BioC] Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'   James W. MacDonald
• [BioC] Can I use Bioconductor to parse *.chp (Affymetrix) files?   James W. MacDonald
• [BioC] Calculating fold change (RG.MA in limma )   ashwin Vishnuvardhana
• [BioC] template matching   Harikrishnadhar
• [BioC] Fwd: template matching   Harikrishnadhar
• [BioC] Can't normalize 300+ HuGene arrays in xps   cstrato
• [BioC] normalising with bad slides   Mark Cowley
• [BioC] Calculating fold change (RG.MA in limma )   Mark Cowley
• [BioC] Calculating fold change (RG.MA in limma )   Mark Cowley
• [BioC] Can't normalize 300+ HuGene arrays in xps   Mike Walter
• [BioC] Munich R Course - Parallel Computing with R   Markus Schmidberger
• [BioC] annotations of Human Gene 1.0 ST microarray and oneChannelGUI   rcaloger
• [BioC] Did the behavior of as.vector(Rle(some.factor)) change on purpose?   Steve Lianoglou
• [BioC] list of annaffy .db files?   Andrew Einhorn
• [BioC] list of annaffy .db files?   Vincent Carey
• [BioC] Job vacancies, University of Cambridge, UK   Krys Kelly
• [BioC] Did the behavior of as.vector(Rle(some.factor)) change on purpose?   Martin Morgan
• [BioC] question regarding MAS5 normalization with reduced probes   James Anderson
• [BioC] Any package like genefilter for NGS?   Xiaohui Wu
• [BioC] list of annaffy .db files?   Marc Carlson
• [BioC] question regarding MAS5 normalization with reduced probes   James W. MacDonald
• [BioC] Limma: topTable without eBayes?   Hooiveld, Guido
• [BioC] question regarding MAS5 normalization with reduced probes   James Anderson
• [BioC] Any package like genefilter for NGS?   Sean Davis
• [BioC] Did the behavior of as.vector(Rle(some.factor)) change on purpose?   Steve Lianoglou
• [BioC] Can't normalize 300+ HuGene arrays in xps   cstrato
• [BioC] Any package like genefilter for NGS?   Xiaohui Wu
• [BioC] question regarding MAS5 normalization with reduced probes   James W. MacDonald
• [BioC] Limma: topTable without eBayes?   Jenny Drnevich
• [BioC] question regarding removing probes/probe sets before normalization   Jenny Drnevich

Last message date: Tue Aug 31 23:57:39 CEST 2010
Archived on: Wed Sep 1 19:37:11 CEST 2010

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