February 2012 Archives by thread
Starting: Wed Feb 1 04:09:01 CET 2012
Ending: Wed Feb 29 23:53:53 CET 2012
Messages: 643
- [BioC] [Rocky] - R code for PGSEA package to identify differentially expressed genes
Valerie Obenchain
- [BioC] Help With RNA-seq
Valerie Obenchain
- [BioC] Can SAM be combined with the bootstrap with replacement method?
Baskaran [guest]
- [BioC] VariantAnnotation updated - error in predictCoding
Lescai, Francesco
- [BioC] converting intensity values to log ratios?
James W. MacDonald
- [BioC] Loading quantiles normalized root data in XPS
Paul Geeleher
- [BioC] subsetting transcriptDb
Juliet Hannah
- [BioC] DESeq on transcripts v/s genes
Abhishek Pratap
- [BioC] converting transcripts to gene level
Abhishek Pratap
- [BioC] DESeq estimateDispersion query
Michal Okoniewski
- [BioC] GCRMA computing affinities error length(prlen) == 1
Tippmann, Sylvia
- [BioC] calculation of probability values from multivariate normal densities
Michał Góralski
- [BioC] TopGO p-values VS DAVID p-values
Paul Geeleher
- [BioC] GEOquery Error
ying chen
- [BioC] Error in gammaFitEM for library(lumi) [Possible Bug]
Chang Jun Park
- [BioC] GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
Cook, Malcolm
- [BioC] FW: GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
Cook, Malcolm
- [BioC] create GeneSetCollection from OBOCollection
Marc Carlson
- [BioC] findOverlaps with strand info
Chris Stubben
- [BioC] [course] CSAMA 2012: Computational Statistics for Genome Biology (Tenth Edition)
stefano iacus
- [BioC] How to specify factors for a RCBD in edgeR
Gordon K Smyth
- [BioC] Problem using KEGGSOAP: multiple genes per identity
January Weiner
- [BioC] Cross-comparison of independent intensities from different experiments (genepix) (sorry I don\'t know how to describe the problem better)
Susanne Gerber [guest]
- [BioC] Trouble in using AgiMicroRna Package
Kannan Venugopal
- [BioC] Updating
Iain Morrison
- [BioC] package to count read prior to DESeq?
nathalie
- [BioC] GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart
Cook, Malcolm
- [BioC] Z-Score Calculation for hgu133plus2 affymetrix microarray.
Murtuza Zair
- [BioC] BaseCounts & edgeR
Gordon K Smyth
- [BioC] error "Too many pushAbortHandlers, can only handle 11" while exporting bedGraph/bigWig using rtracklayer from Bioconductor
Cook, Malcolm
- [BioC] Proxy setting for R/Bioconductor
Karthik
- [BioC] Microarray: correlation and Rgraphviz
CAM HABI
- [BioC] Adjusting removeBatchEffect from limma
Gordon K Smyth
- [BioC] Installing AgiMicroRna Package
Karthik K N
- [BioC] Limma question_Intra-Spot Correlation Question
jgomez at uni-potsdam.de
- [BioC] DEseq
saikouy bah
- [BioC] Issues with AgiMicroRna filtering step (Error in is(ddNORM, "uRNAList") : object 'ddNORM' not found)
Karthik K N
- [BioC] Exporting results from AgiMicroRna to GeneSpring GX
Karthik
- [BioC] annotaion package
Bidisha Mitra
- [BioC] Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!
Benjamin Høyer
- [BioC] Important: Help with eBayes in AgiMicrRna and on how to find differentially expressed genes
Karthik K N
- [BioC] baySeq
Tina Asante Boahene
- [BioC] BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart
Cook, Malcolm
- [BioC] Rsubread installation failed.
Sang Chul Choi
- [BioC] Error reading cel files using Readaffy() or getGEO()
Salwa [guest]
- [BioC] narrow on GappedAlignments fails with error
Hervé Pagès
- [BioC] edgeR for paired-end and strand specific data
wang peter
- [BioC] Fw: annotaion package
Bidisha Mitra
- [BioC] Rsamtools installation error
Wolfgang Raffelsberger
- [BioC] easyRNASeq - error reading single chromosome bam
Lescai, Francesco
- [BioC] Problem while installing \"org.At.tair.db\" and \"ath1121501.db\"
Reetu [guest]
- [BioC] Limma: questions about data pre-processing
Vladimir Krasikov
- [BioC] Two populations on microarray
Ben Tupper
- [BioC] Is anyone using affylmGUI for Affy Exon 1.0 analysis?
Alan Derr
- [BioC] SOM clustering
Tanay Ghosh [guest]
- [BioC] How do I define my design in FDR-AME package
Yu Chen [guest]
- [BioC] Rgraphviz: cannot allocate memory block of size 3.4 Gb
Matthew Pettis
- [BioC] [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart
Cook, Malcolm
- [BioC] FDR (False Discovery Rate)
Tina Asante Boahene
- [BioC] Separating channels of a two-color microarray
January Weiner
- [BioC] NormqPCR and ReadqPCR
Pepijn Kooij
- [BioC] flowFlowJo error
Gabriel Kaufman
- [BioC] GenomeGraphs question
Iain Gallagher
- [BioC] How to install topGO on R version 2.14.0
gabriel [guest]
- [BioC] Error message with RNAither
Catherine Garry
- [BioC] Genomicfeatures chromosome names matching
Hervé Pagès
- [BioC] report a possible bug of edgeR
wang peter
- [BioC] iFlow error messages
Gabriel Kaufman
- [BioC] DESeq and transcript-wise analysis
Elena Sorokin
- [BioC] DEGseq help
Tina Asante Boahene
- [BioC] GenomicFeatures::makeTranscriptDbFromGTF?
Steve Lianoglou
- [BioC] February-March 2012 ***R/S-PLUS Courses***by XLSolutions Corp at 9 USA locations
sue at xlsolutions-corp.com
- [BioC] suggestions/comments on DESeq transcript wise analysis
Akula, Nirmala (NIH/NIMH) [C]
- [BioC] Optimisation
Simon Noël
- [BioC] how can i convert a gse object(expression sets) to affybatch
Salwa Eid
- [BioC] Import sequences from MacClade 4.*
Brian
- [BioC] RE : maping SNPs
Simon Noël
- [BioC] Removing probes with low variance across samples (Infinium 450k)
khadeeja ismail
- [BioC] Using write.table with output from topTags [was: report a possible bug of edgeR]
Gordon K Smyth
- [BioC] limma barcodeplot with 2 groups
Dario Strbenac
- [BioC] bioMart
Bogdan Tanasa
- [BioC] Inconsistent coefficient values
Richard Coulson [guest]
- [BioC] a problem in reading in cel files
Manuela Di Russo
- [BioC] GOSeq error
Iain Gallagher
- [BioC] Finding the similarity of two microarray experiments
blockaa at huskers.unl.edu
- [BioC] Integer overflow when summing an 'integer' Rle
Nicolas Delhomme
- [BioC] about library size and length of gene information in DEseq
wang peter
- [BioC] Open Position :: Postdoc in systems genetics in Cambridge
Florian Markowetz
- [BioC] Empty RangedData with value columns?
Robert Scharpf
- [BioC] gene function assessment
Abhishek Pratap
- [BioC] gplots Heatmap
Polikepahad, Sumanth
- [BioC] DEXseq: Making exonCountSet object
Elena Sorokin
- [BioC] Rsubread/Rsamtools mappings outside of chromosome ranges
Thomas Girke
- [BioC] Help baySeq
Tina Asante Boahene
- [BioC] AB Rat Genome Survey Microarray
Iain Gallagher
- [BioC] using easyRNASeq examples
Nicolas Delhomme
- [BioC] impute package
Wendy Yim
- [BioC] Probe include snp in HG-U133_Plus_2
Fabrice Tourre
- [BioC] question about normalization of RNAseq by tweeDEseq using TMM from edgeR
Sermsawat Tunlaya-Anukit
- [BioC] missing probe_id in ath1121501.db
Stefan Bleuler
- [BioC] Bioconductor Digest, Vol 108, Issue 12
Alejandro Reyes
- [BioC] GenomicRanges requires a IRanges version not available in the repository
Juan L. Mateo
- [BioC] relationship between Fold Change and SLR
Laura Bermúdez
- [BioC] Creating a customized cut flow with the affy/limma packages
J.M.Jensen [guest]
- [BioC] DeSeq vs current version of Cuffdiff
Richard Friedman
- [BioC] iSeq package\'s peakreg fails
Lauri Lyly [guest]
- [BioC] SNP6 data to VCF
Sean Davis
- [BioC] Inquiry package for Illumina BeadChip HumanOmni
Jiang [guest]
- [BioC] Installing GenomicRanges require a version of IRanges unavailable
Duhaime Johanne
- [BioC] BSgenome installation error
Mohamed Radhouane Aniba
- [BioC] DESeq dispersions for series
Willie Nelson
- [BioC] Affymetrix internal control up-regulated, is anything wrong?
Michele Bellesi [guest]
- [BioC] Red line in MAplots, is it lowess or smooth.spline?
Ali Mohammadian
- [BioC] [lumi] methylumIDAT : probleme to read idat files
Dylan Aïssi [guest]
- [BioC] Help to access hapmap using biomart
MLSC
- [BioC] clippda: a package for clinical proteomics data analysis
Stephen Nyangoma
- [BioC] number of genes for DESeq analysis
vladimir mashanov
- [BioC] SNPlocs package for dbSNP 135
Hervé Pagès
- [BioC] edgeR: GLM & residuals and model fitting & hypothesis testing
Susanne Franssen
- [BioC] Poisson noise with respect to digital gene expression
Dave Tang
- [BioC] IlluminaMousev2.db probe quality information questions?
Lourdes Peña Castillo
- [BioC] Possible bug in sva package regarding ComBat and use of numCovs
Djie Tjwan Thung
- [BioC] Error in readSeqFile of qrqc package?
Sang Chul Choi
- [BioC] how to set library size in DESeq?
wang peter
- [BioC] arrayQualityMetrics package - bugs and errors
Vladimir Krasikov
- [BioC] Siggenes SAM analysis: log2 transformation and Understanding output
David Westergaard
- [BioC] How to plot NGS data?
Bernd Jagla
- [BioC] how to update DEseq package on windows?
wang peter
- [BioC] Compensating using spillover function of flowCore
John Pura
- [BioC] Biostrings - pairwiseAlignment trimmed pattern returned
Erik Wright
- [BioC] a problem to install bioconductor on 2.14
wang peter
- [BioC] Estimating fold change from limma 'log2FC' using lumi vst instead of log2 transformation?
Ross
- [BioC] meta-analysis with RankProd
Barbara Shih
- [BioC] Gettin Expressions back from MA.List
Ali Mohammadian
- [BioC] htSeqTools errors
Juan L. Mateo
- [BioC] 'which' argument to readGappedAlignments
Juliet Hannah
- [BioC] 17th Summer Institute in Statistical Genetics, Seattle, July 9-27
Stephanie M. Gogarten
- [BioC] SCIENTIFIC DATA CURATOR / 40 HOUR / DAY / BWH - CHANNING LABORATORY
Brigham and Women's Hospital [guest]
- [BioC] IS PROGRAMMER/ANALYST I / 40 HOUR / DAY / BWH - CHANNING LABORATORY
Brigham and Women's Hospital [guest]
- [BioC] DEXseq: fitDispersionFunction error
Elena Sorokin
- [BioC] Estimating fold change from limma 'log2FC' using lumi
Gordon K Smyth
- [BioC] edgeR: GLM - adjusting for unwanted effect?!
Lina Weber
- [BioC] use of duplicateCorrelation in Limma with agilent one-color arrays
Jabez Wilson
- [BioC] EBImage package
Jordi van Gestel
- [BioC] LIMMA => 1000 samples vs 3 samples
Daniel
- [BioC] qcplot() error in methylumi?
Aaron Mackey
- [BioC] convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)
Aaron Mackey
- [BioC] how to remove affymetrix control probe sets from a an expression set
Salwa Eid
- [BioC] Removing phenoData and assayData
tyrone [guest]
- [BioC] Installation errors for DESeq, Genomic Ranges etc.
Alpesh Querer
- [BioC] ChIPpeakAnno
Brian James Gadd
- [BioC] Agilent 8x60K Gene Expression Package
Karthik K N
- [BioC] Deferential gene expression databases
saikouy bah
- [BioC] Add extra columns to GRanges Metadata
Paul Leo
- [BioC] Help for snpMatrix
MLSC
- [BioC] Reading 5000 celfiles with ReadAffy
Saif Ur-Rehman [guest]
- [BioC] limma: to pair or not to pair?
Aaron Mackey
- [BioC] Limma normalizeBetweenArrays When Samples Have Different Distributions
Dario Strbenac
- [BioC] Testing for differential expression variability with edgeR
Miguel Gallach
- [BioC] Standard error and confidence intervals in DESeq?
Akula, Nirmala (NIH/NIMH) [C]
- [BioC] coefficient of variation for Agilent chip log ratio data
array chip
- [BioC] tapply for enormous (>2^31 row) matrices
Matthew Keller
- [BioC] Use probesets with highest baseline expression for differntial gene expression in LIMMA
Ekta [guest]
- [BioC] makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : , bind.data must have non-zero dimensions
mabawsa
- [BioC] BiomaRt error: server down?
Lisa Hopcroft
- [BioC] Finding coding SNPs with predictCoding
Alex Gutteridge
- [BioC] Job openings: Staff Scientist - Computational Biology and Bioinformatics - Massachusetts General Hospital
Wittner, Ben, Ph.D.
- [BioC] warning in lumi
Francesco Mancuso
- [BioC] Experience with using the 'affy' package (v1.28.1) to perform QC on Affymetrix PrimeView human arrays
Daniel Hurley
- [BioC] GO Analysis for Mouse Exon Array
Dai, Hongying,
- [BioC] [R] tapply for enormous (>2^31 row) matrices
Matthew Keller
- [BioC] segfault when using data.table package in conjunction with foreach
Matthew Keller
- [BioC] OS X 10.7.x "Lion"
Tom Keller
- [BioC] Use probesets with highest baseline expression for differntial gene
Gordon K Smyth
- [BioC] Limma package for Agilent microarray Image Analysis
Karthik K N
- [BioC] how split a matrix
Ali Mohammadian
- [BioC] PostForm() with KEGG
Ovokeraye Achinike-Oduaran
- [BioC] making use of the Apis mellifera BeeBase assembly 4 data in goseq
Hervé Pagès
- [BioC] Error in GAGE analysis
Javerjung Sandhu
- [BioC] Error in GAGE analysis, help URGENTLY required
Javerjung Sandhu
- [BioC] Goseq plot
Alpesh Querer
- [BioC] miRNA- KEGG
Ali Mohammadian
- [BioC] reference letter for R/Bioconductor
Zhi Zhang
- [BioC] Help with promoter analysis
Davy
- [BioC] statistical test help -RT-PCR data?
John Alexander
- [BioC] Volcano plot
saikouy bah
- [BioC] heatmap.2 with different colour ranges
Wendy Qiao
- [BioC] Odd warning in simpleaffy, using quality control
David Westergaard
- [BioC] how to cluster transcripts of one gene
wang peter
- [BioC] arrayQualityMetrics: huge object size!?
Shi, Tao
- [BioC] Making use of the Apis mellifera assembly 2 data in goSeq
Corby, Vanessa
- [BioC] newbie subset question
Tom Keller
- [BioC] convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
karlerhard at berkeley.edu
- [BioC] how to get gene list for given GO terms?
Ou, Jianhong
- [BioC] Strand information for dbSNP packages
Alex Gutteridge
- [BioC] problems with "cannot allocate vector of size.."
Manuela Di Russo
- [BioC] Aroma query (Follow up to thread: \"Reading 5000 celfiles with ReadAffy\" )
Saif Ur-Rehman [guest]
- [BioC] report a possible bug of
wang peter
- [BioC] GAGE heatmap pdf question...
Alan Derr
- [BioC] dbSNP strand information
Alex Gutteridge
- [BioC] problem creating own org.Ss.eg.db
Hooiveld, Guido
- [BioC] GAGE Question
Javerjung Sandhu
- [BioC] GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
Javerjung Sandhu
- [BioC] getGEO error?
Hendrik Falk
- [BioC] countOverlaps within Mode Counting
Dario Strbenac
- [BioC] Warning of function "ncbiTaxonomy"
吴春燕
- [BioC] beadarray vignette has broken code in R2.14.1?
Henriquez, Nick
- [BioC] summarizeOverlaps vs countOverlaps
swaraj basu
- [BioC] about GO analysis
Zhi Zhang
- [BioC] adding factors to a data frame from a dataframe
Tom Keller
- [BioC] reading with lumi
Ed Siefker
Last message date:
Wed Feb 29 23:53:53 CET 2012
Archived on: Sat Mar 3 09:44:27 CET 2012
This archive was generated by
Pipermail 0.09 (Mailman edition).