August 2010 Archives by thread
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] Human Affymetrix Exon microarrays
Jinyan Huang
- [BioC] Odd Plotting Behavior with lymphGate flowStats
Nishant Gopalakrishnan
- [BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Samantha England
- [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] Bioconductor Digest, Vol 90, Issue 1
Amos Folarin
- [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] 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] [R] error with ReadAffy()
James W. MacDonald
- [BioC] Illumina GoldenGate methylation array, methylumi
Jinyan Huang
- [BioC] EBImage not loading
Henrik Failmezger
- [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] 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] [R] error with ReadAffy()
Amos Folarin
- [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A
Glazko, Galina
- [BioC] dynamic range/scale using exprs (Biobase)
Lucia Peixoto
- [BioC] Analysis: two-color, time series
Gordon K Smyth
- [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] entrez gene to genome coordinates
Bhatti, Gaurav
- [BioC] Bioconductor Developer Meeting Europe - 17.-18. 11. 2010
Wolfgang Huber
- [BioC] 'plgem' package bug fix
Pavelka, Norman
- [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] 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] [limma] Separate Channel Analysis of 2 color data with summarization
Ana Conesa
- [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] Problem with bnlearn and Rgraphviz
hcong at cs.usm.my
- [BioC] append on DNAStringSet produces an empty DNAString as last element
Philip Kensche
- [BioC] error in makeTranscriptDbFromUCSC of library(GenomicFeatures)
Yuan Jian
- [BioC] Another limma factorial that needs controlling and pairing
sabrina
- [BioC] Bacterial genomics
Mathieu Parent
- [BioC] SPIA with Mouse Data
Will Bush
- [BioC] error with getMeasureRepAgreement()
Ning
- [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] 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] TranscriptDb and genomicranges questions
Hervé Pagès
- [BioC] Long Time Series analysis
Xiaokuan Wei
- [BioC] KEGG orthology linking (K numbers )?
Fabian Grammes
- [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] How to normalize one additional CEL file?
Wiktor Mazin
- [BioC] Help to confirm Design matrix and Between array Normalization.
Veerendra GP
- [BioC] mypeaklist in ChIPpeakAnno
Zhu, Julie
- [BioC] TranscriptDb and genomicranges questions
Hervé Pagès
- [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] Advise on setting up a non-specific filter for differential expression
Lucia Peixoto
- [BioC] limma, contrasts, and NA's
Albyn Jones
- [BioC] error when loading galgo package
Qian Liu
- [BioC] Normalization of polyA RNA-seq?
Xiaohui Wu
- [BioC] Help to confirm Design matrix and Between array Normalization
Gordon K Smyth
- [BioC] how does limma calculate the coefficients with using different design matrix?
Xiaokuan Wei
- [BioC] how does limma calculate the coefficients with using different design matrix?
Gordon K Smyth
- [BioC] Advise on setting up a non-specific filter for differential expression
Tobias Straub
- [BioC] mypeaklist in ChIPpeakAnno
Zhu, Julie
- [BioC] Advise on setting up a non-specific filter for differential expression
Lucia Peixoto
- [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] unmapped keys in hugene10stprobeset.db
Paul Shannon
- [BioC] genArise
mcarvajal at ifc.unam.mx
- [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
Tobias Straub
- [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] 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] Error in package goseq
Joydeep Mitra
- [BioC] average difference and global scaling for normalizing affymetrix expression data?
Alice Johnstone
- [BioC] get position information for different gene/transcript IDs
shirley zhang
- [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] mypeaklist in ChIPpeakAnno
Zhu, Julie
- [BioC] using smoothX in Ringo
Joern Toedling
- [BioC] R Courses***September - October 2010 schedule by XLSolutions Corp
Sue Turner
- [BioC] Help on experiment design
Marcelo Brandão
- [BioC] Reading image file from ImaGene 9.0
Gordon K Smyth
- [BioC] boxplot labels vertical?
Andrew Einhorn
- [BioC] Bioconductor-EBImage problem
Xiushan Yin
- [BioC] Creating a custom chromLocation object for cPlot
Michael Muratet
- [BioC] heatmap 'contrast': suggestions for a zlim adjustment in heatmap.2
Karl Brand
- [BioC] Circular binary segmentation for allele-specific CN data
Christine Ho
- [BioC] Fastest way to read CSV files
Gaston Fiore
- [BioC] Fastest way to read CSV files
Sean Davis
- [BioC] R/biomaRt problem
will.eagle at gmx.net
- [BioC] xps: root.profile on a asubset of the data
Daniel Brewer
- [BioC] Error: cannot allocate vector of size 649.8 Mb
Marco Ortiz
- [BioC] IRanges::Rle and missing values
Kasper Daniel Hansen
- [BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?
Steve Lianoglou
- [BioC] Error: cannot allocate vector of size 649.8 Mb
Martin Morgan
- [BioC] biomaRt and hapmap "virtualSchema" parameter mis-specification
Andrew McDavid
- [BioC] Error: cannot allocate vector of size 649.8 Mb
Martin Morgan
- [BioC] IRanges: interaction with model fitting
Kasper Daniel Hansen
- [BioC] Limma -time course - no replicates
Yair Benita
- [BioC] Difficulties updating Biostrings on Ubuntu
Erik Wright
- [BioC] gene2pathway retrain: which model is more complete?
Bogdan
- [BioC] Advice on a linkage program
Paul Leo
- [BioC] gene2pathway retrain: which model is more complete?
Bogdan
- [BioC] Fst - sequence data
blue jay
- [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] downloading different kinds of microarray data
Sean Davis
- [BioC] downloading different kinds of microarray data
Alex Levitchi
- [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] endoapply over GRangesList fails when an empty GRanges object is returned (Bug?)
Steve Lianoglou
- [BioC] error in RG.MA in limma
ashwin Vishnuvardhana
- [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] Why is *ply-ing over a GRangesList much slower than *ply-ing over an IRangesList?
Steve Lianoglou
- [BioC] Biobase: How to replace the ExpressionSet phenoData?
Daniel Brewer
- [BioC] illumina Infinium HumanMethylation27 detection-p-value
Pan Du
- [BioC] annotation for new agilent arrays
axel.klenk at actelion.com
- [BioC] Agi4x44PreProcess- RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)
Brown, Joseph
- [BioC] Differential expresson in more than 2 samples using NGS?
Gordon K Smyth
- [BioC] Scan not respecting what
Gaston Fiore
- [BioC] about normalizeMethyLumiSet
gregory voisin
- [BioC] post-hoc test after F-test in Limma
Christina Orsmark-Pietras
- [BioC] question regarding MAS5 normalization with reduced probes
James Anderson
- [BioC] Parallel Computing of varSelRF and tuneRF
Min Wang
- [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] Subscripting GenomicRanges objects with [[ or $
Tim Yates
- [BioC] Can't normalize 300+ HuGene arrays in xps
Mike Walter
- [BioC] Genominator problem
Johnny H
- [BioC] Fwd: Genominator problem
Johnny H
- [BioC] how to find probes' names in probeset
Glazko, Galina
- [BioC] Limma script - Opinions requested
Orfe, Lisa
- [BioC] E. coli annotation to map?
Rayna
- [BioC] Heatmap with 7120x500 array
Gaston Fiore
- [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] AgiMicroRna and readMicroRnaFE
Paulo Nuin
- [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] 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] normalising with bad slides
Andrew Einhorn
- [BioC] Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'
Kristel van Eijk
- [BioC] Can I use Bioconductor to parse *.chp (Affymetrix) files?
Anton Kratz
- [BioC] to know about the reason in results obtained using DESeq and cufflinks
Aniket Vatsya
- [BioC] superimpose lowess on smoothScatter
Andrew Einhorn
- [BioC] Calculating fold change (RG.MA in limma )
ashwin Vishnuvardhana
- [BioC] template matching
Harikrishnadhar
- [BioC] normalising with bad slides
Mark Cowley
- [BioC] Calculating fold change (RG.MA in limma )
Mark Cowley
- [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] Job vacancies, University of Cambridge, UK
Krys Kelly
- [BioC] Any package like genefilter for NGS?
Xiaohui Wu
- [BioC] Limma: topTable without eBayes?
Hooiveld, Guido
- [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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