May 2012 Archives by thread
Starting: Tue May 1 02:27:04 CEST 2012
Ending: Thu May 31 23:53:42 CEST 2012
Messages: 599
- [BioC] Design and not estimable coefficients
Gordon K Smyth
- [BioC] Question regarding COA plot generated by made4 package
Valerie Obenchain
- [BioC] beadarray package: question about processSwathData() segmentHeight and segmentWidth values
bzguan at ucdavis.edu
- [BioC] beadarray package: problem finding Illumina annotation for Human660w_quad bead chip
bzguan at ucdavis.edu
- [BioC] Copy Number Analysis across multiple SNP array plaforms
Ed Schwalbe
- [BioC] DESeq
Natasha Sahgal
- [BioC] GRangesList filtering
Halian Vilela
- [BioC] question with reading bead summary data into beadarray
Ou, Jianhong
- [BioC] Problem creating expression set.
dha 2001
- [BioC] How do I find up and down regulated genes for each contrast in LIMMA?
Paul, Cristina
- [BioC] Questions: How to convert egt file to txt
JiangZhengyu
- [BioC] BSgenomes and protein sequences
Zybaylov, Boris L
- [BioC] combining hgu133a and hgu133b
Steve Lianoglou
- [BioC] Odd behaviour with renameSeqlevels
Alex Gutteridge
- [BioC] Limma analyses;paired and/or factorial design?
john herbert
- [BioC] stable gene in microarray
Marco Fabbri
- [BioC] Help strange GSEA error
Martin Morgan
- [BioC] R IDE editor
Yue Li
- [BioC] Fwd: [Bioc-devel] Changes in the %in% function for DNAStringSet?
Nicolas Delhomme
- [BioC] basics of GLMFit
chris Jhon
- [BioC] Problem with "ragene10stprobeset.db" package
Laura Bermúdez
- [BioC] Error loading charm
Francesco Mancuso
- [BioC] Job posting: Computational Biologists/Bioinformaticians, University of Cambridge, UK
Krys Kelly
- [BioC] KEGG pathway heat map
Felipe Riveroll Aguirre
- [BioC] Full error messages?
Ed Siefker
- [BioC] May-July 2012 ***R/S-PLUS Courses***by XLSolutions Corp at 9 USA locations
sue at xlsolutions-corp.com
- [BioC] FW: How do I find up and down regulated genes for each contrast in LIMMA?
Paul, Cristina
- [BioC] minfi -- now what?
Ed Siefker
- [BioC] Question regarding MADE4 graphs
aedin culhane
- [BioC] normalize GFP expression by cell size and graph with densityplot
Chandra Jack
- [BioC] question regarding ChIPPeakAnno use
Zhu, Lihua (Julie)
- [BioC] how to get plant taxonomy
wang peter
- [BioC] NuIDs not found
Ed Siefker
- [BioC] problem with makeFeatureDbFromUCSC and snp135Common track
Tim Triche, Jr.
- [BioC] Convert gene symbols to ensembl id
michelle_low
- [BioC] Adding a column to phenoData dataframe
ieee529 contact
- [BioC] LIMMA: plotMDS
Kripa R
- [BioC] Top 10% of genes based on p-value in TopTable
Ovokeraye Achinike-Oduaran
- [BioC] FDR calculation for expression array
JiangZhengyu
- [BioC] gene set enrichment analysis of RNA-Seq data
Paolo Guarnieri
- [BioC] miRNA annotation
Wu, Huiyun
- [BioC] edgeR outlier question
Simon Melov
- [BioC] BSgenomes and protein sequences: protein names
Zybaylov, Boris L
- [BioC] Re-send directly to BioC on miRNA annoation
Wu, Huiyun
- [BioC] how to unlist a list of GappedAlignments objects
Yue Li
- [BioC] normalize.AffyBatch.vsn with reference vsn object
R Tagett
- [BioC] outlier probes detection
andrea.grilli at ior.it
- [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Juan Fernández Tajes
- [BioC] export a GappedAlignment object to a BAM file
Yue Li
- [BioC] FW: miRNA annotation
Wu, Huiyun
- [BioC] [Bioc-devel] technical and biological replicates in the same Exprset - Agi4x44
James W. MacDonald
- [BioC] question about BSgenome and C.pombe genome, absent in USCS
Hervé Pagès
- [BioC] BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)
Hervé Pagès
- [BioC] R / Maanova: contrasts for interaction in model with 2 fixed factors
V. Oostra
- [BioC] Moderated t-test
Chintanu
- [BioC] Human Illumina Methylation27k question
Juan Fernández Tajes
- [BioC] Limma: Top 10% gene list based on p-values
Ovokeraye Achinike-Oduaran
- [BioC] GO analysis for CNVs
Yadav Sapkota
- [BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
Marie Sémon
- [BioC] DESeq Package Questions
Xin Davis
- [BioC] Open PhD Position - Bioinformatics in collaboration with SAP
Amin Moghaddasi
- [BioC] tilingArray normalizeByReference Data Scaling
Dario Strbenac
- [BioC] technical and biological replicates in the same Exprset - Agi4x44
Gordon K Smyth
- [BioC] eset -Affy Mouse Gene 1.0 ST. Array-
alessandro brozzi
- [BioC] ReadAffy() Error - 2 Platforms in one file
Ovokeraye Achinike-Oduaran
- [BioC] BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?
Martin Johnsson
- [BioC] Problem using biomaRt to retrieve human SNPs given a list of gene symbols
Yong Li
- [BioC] Outcome~predictor model evaluation, repeated measurements
rad mac
- [BioC] FOSBE 2012
Douglas Murray
- [BioC] v is for values()
Tim Triche, Jr.
- [BioC] How to use DESeq output to convert raw counts to normalized data
Xin Davis
- [BioC] EdgeR exactTest - treatment names determine sign of fold change
Spollen, William G.
- [BioC] Random Forest Code
Bahar AZ
- [BioC] Building specific Ortoghonal contrasts in LIMMA
Garcia Orellana,Miriam
- [BioC] ChIPPeakAnno query (overlaps)
Zhu, Lihua (Julie)
- [BioC] BiomaRt returns empty set for getBM for celegans miRNA
Zhu, Lihua (Julie)
- [BioC] Extracting topTable data from saved file
Ovokeraye Achinike-Oduaran
- [BioC] Correcting for batch effects in limma
khadeeja ismail
- [BioC] Limma, design matrix, lmfit Coefficients not estimable error
Varshna Goelela
- [BioC] Finding coding SNPs with predictCoding
Valerie Obenchain
- [BioC] error under "hclust" for expression data
Wang, Li
- [BioC] Recommend some R packages source code to read.
Fabrice Tourre
- [BioC] fitting growth curve
Andreia Fonseca
- [BioC] TEQC see all the reads with a given coverage
nathalie
- [BioC] Help with adSplit package
Luz Mayela Soto
- [BioC] necessity of moderated t statistic and false discoveries for small predefined gene list?
Richard Friedman
- [BioC] error running makeProbePackage
Zhang, Jian
- [BioC] 450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Bartlett, Thomas
- [BioC] miRNA and other small RNAs
Wu, Huiyun
- [BioC] subreddit for R related stuff
Robert M. Flight
- [BioC] iSeq Peak Position
Dario Strbenac
- [BioC] BiomaRt error: server down?
Lisa Hopcroft
- [BioC] edgeR input and design matrix help
KJ Lim
- [BioC] ChIPpeakAnno annotatePeakInBatch
Zhu, Lihua (Julie)
- [BioC] Query neighboring genes
Yadav Sapkota
- [BioC] Excessive memory requirements of PING or bug?
Lars Hennig
- [BioC] Package for doing Copy number analsysi with LOH
Rajan Saini
- [BioC] edgeR : input and design matrix help
KJ Lim
- [BioC] Using BrainArray mappings with oligo package
Steve Piccolo
- [BioC] BioC 2012
Valerie Obenchain
- [BioC] how to design matrix by edgeR
wang peter
- [BioC] GSEA with methylation data
Tim Smith
- [BioC] Rsamtools: scanBamFlag bug?
Nuno Fonseca
- [BioC] PANTHER in R.... Gene lists in sigPathway?
Ovokeraye Achinike-Oduaran
- [BioC] edgeR, comparing models
Alpesh Querer
- [BioC] limma all adj.P.Val the same
Sam McInturf
- [BioC] PWMscoreStartingAt and ambiguous subject seqs
Janet Young
- [BioC] PWMscoreStartingAt and ambiguous subject seqs
Hervé Pagès
- [BioC] PWMscoreStartingAt and ambiguous subject seqs
Janet Young
- [BioC] PWMscoreStartingAt and ambiguous subject seqs
Janet Young
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
Martin Morgan
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
Martin Morgan
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
Martin Morgan
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
omranian
- [BioC] Error in .testGOFrame(x, organism)
Martin Morgan
- [BioC] how to design a model matrix
wang peter
- [BioC] help with mapping statistics summary
Leonor Carvalho
- [BioC] aCGH package. Plots: X axis label problems
Sarah JugurnauthLittle
- [BioC] Useful information about Ensembl release 67 mart databases
Thomas Maurel
- [BioC] GOSim yeast
Fred Hoffman [guest]
- [BioC] Euler diagram (Venn diagram)
pankaj borah
- [BioC] GO analysis using chromosomal ranges
Yadav Sapkota
- [BioC] build/check reports for ENVISIONQuery, IdMappingRetrieval on OSX
Day, Roger S
- [BioC] limma p-value calculated how?
Kripa R
- [BioC] question about how analysis affymetrix huex st array
Ou, Jianhong
- [BioC] How to make Illumina cluster files from HapMap
JiangZhengyu
- [BioC] cell cycle modeling
Anja Mirenska
- [BioC] Create A Stranded probeAnno Object
Dario Strbenac
- [BioC] design and contrast matrix for limma time series without replicates
shao chunxuan
- [BioC] File format for single channel analysis of Agilent microarray data with Limma?
Parisa [guest]
- [BioC] Problem running HumMeth27QCReport after upgrading R to 2.15
Niles Oien [guest]
- [BioC] methylumi on Infiniium27k idat files
chris briggs
- [BioC] Genes to SNPs Tool
Ovokeraye Achinike-Oduaran
- [BioC] problem with large logFC value
sgonzalez at ira.cinvestav.mx
- [BioC] EdgeR: problem with large logFC value
sgonzalez at ira.cinvestav.mx
- [BioC] xvalSpec('NOTEST') problem
Gustavo Fernández Bayón
- [BioC] edgeR: design matrix
KJ Lim
- [BioC] Fwd: heatmap.2 question
Alyaa Mahmoud
- [BioC] findOverlaps question from a newbie...
gowtham
- [BioC] 'citation("RBGL")' command produces package not found error
Jeremiah Willcock
- [BioC] easyRNASeq Error in counting from C.elegans
Yonggan Wu
- [BioC] suppressMessages does not work with endoapply?
Yue Li
- [BioC] how to rank affy probesets by their probe-effect magnitude
Leo Lahti
- [BioC] DESeq error with glm.fit during estimateDispersions
chris_utah
- [BioC] FastqStreamer
Marcus Davy
- [BioC] voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Tim Triche, Jr.
- [BioC] easyRNAseq question
Nicolas Delhomme
- [BioC] Expt. design question on optimal number of replicates (in edgeR or else where)
gowtham
- [BioC] GEOquery loading error
Jian Zhang [guest]
- [BioC] DESeq error thrown during estimateDispersions w/ coxReid method
Simon Anders
- [BioC] How to identify DE genes by comparing two groups where one contains a single array data
Lei Li [guest]
- [BioC] Rsubread package usage and speed questions
Davis, Wade
- [BioC] error installing Rgraphviz
Mark Miller
- [BioC] HTqPCR
Heidi Dvinge
- [BioC] how to make interactive search by edgeR
narges [guest]
- [BioC] beadarray package - analysis of bead summary level data
Yehudit Hasin [guest]
- [BioC] biomart error returning data
Alasdair Jubb [guest]
- [BioC] edgeR: topTags
KJ Lim
- [BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")
Simone [guest]
- [BioC] remove.dupEntrez from nsFilter{genefilter}
Klemens Vierlinger [guest]
- [BioC] GEOquery install problem with openSUSE 11.4 and R 2.15
Bartlett, Thomas
- [BioC] useDevel() not working
Michael Muratet
- [BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?
Sang Chul Choi
- [BioC] Amplicon and exon level read counts and GC content
Yu Chuan Tai
- [BioC] Newbie. quantile normalization should be done on all conditions or within replicates of each condition?
Cytochalasin
- [BioC] GRanges Constructor With seqlengths
Dario Strbenac
- [BioC] MacOS Package installation problems
Michael Salbaum
- [BioC] topGO dependency: Rgrapphviz
Thompson, Kevin
- [BioC] Cannot call ShortRead package FastqSampler from Linux
talshay
- [BioC] samtools error
Yu Chuan Tai
- [BioC] DEXSeq filtering
mali salmon
- [BioC] DESeq estimateDispersions() problem
Karl Lundén
- [BioC] Errors Installing Package qrqc under MacOsX
Sue Jones
- [BioC] how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer
Yue Li
- [BioC] BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
Oliver Ruebenacker
Last message date:
Thu May 31 23:53:42 CEST 2012
Archived on: Fri Jun 1 00:50:56 CEST 2012
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