June 2011 Archives by thread
Starting: Wed Jun 1 01:26:37 CEST 2011
Ending: Thu Jun 30 22:12:29 CEST 2011
Messages: 461
- [BioC] edgeR - multiple comparisions
Davis McCarthy
- [BioC] How can I read a WIGGLE file into R
Yanchun Bao
- [BioC] readQpcrBatch()
John Coulthard
- [BioC] PreFiltering probe in microarray analysis
Stephanie PIERSON
- [BioC] DNA copy ploting function
Nathalie Conte
- [BioC] About the installation of ChIPsim
Vincent Carey
- [BioC] DNAcopy dev version installation problem
Zhu, Lihua (Julie)
- [BioC] lumi and plotHousekeepingGene
Janet Young
- [BioC] vennSelect error
mali salmon
- [BioC] XPS crashes
Clara Pons
- [BioC] clustering of expression data
sanchita 0804
- [BioC] Lumi methylation analysis errors in lmFit
Jasreet
- [BioC] maSigPro and "subscript out of bounds"
Valerie Obenchain
- [BioC] Error from aafGO using yeast2.db
James W. MacDonald
- [BioC] "leading minor...is not positive definite" in flowStats warpSet() function
Hill, Andrew
- [BioC] Grouping data in a heatmap
Mark Aquino
- [BioC] edgeR users update to v2.2.5
Davis McCarthy
- [BioC] biomaRt- too many attributes selected
Lavinia Gordon
- [BioC] quantile normalization+limma package
samane fazeli
- [BioC] Limma; matrix of microarray data and design matrix
john herbert
- [BioC] question about mt.maxT output (multtest)
Les Dethlefsen
- [BioC] Rgraphviz: Reproduce node layout from fdp
Gregory C Imholte
- [BioC] AffyProbeMiner Mouse 4302 geneccds CDF file
Benjamin Otto
- [BioC] BLAST in R
Zoha Moztarzadeh
- [BioC] a bug in the function pamr.plotcen()
Alogmail2 at aol.com
- [BioC] Sliding window t-test?
Tim Smith
- [BioC] CALCULATION OF P VALUE
sanchita 0804
- [BioC] Significance of variance
Nitish Kumar Mishra
- [BioC] miRNA microarray analysis
Assa Yeroslaviz
- [BioC] arrayQuality - maQualityPlots - Error: duplicate switch defaults: 'list(dev =...' and ''
Fabio Liberante
- [BioC] removing packages from the workspace - is this ok?
J.delasHeras at ed.ac.uk
- [BioC] rtracklayer error?
Tim Smith
- [BioC] Calling R from php
Fahim Mohammad
- [BioC] 4-way venn diagram with ChIPpeakAnno
Zhu, Lihua (Julie)
- [BioC] lumi, Illumina Methylation 450k, and robust methylation calls
Tim Rayner
- [BioC] CGHcall and Normalization
Salih Tuna
- [BioC] Use of individual channel from a 2-color array as a measure of expression level?
Hari Easwaran
- [BioC] dealing with negative values in illumina
Arno, Matthew
- [BioC] BSgenome package - danRer7 genome assembly
Hervé Pagès
- [BioC] IRanges package: findOverlaps on blobs
Hervé Pagès
- [BioC] Fw: a bug in heatmap.plus?
Shi, Tao
- [BioC] DAT files
Aleksandra ..
- [BioC] meet problem when use rtracklayer
Yanchun Bao
- [BioC] Regarding GEOquery
Nitish Kumar Mishra
- [BioC] biomaRt: using a list as values. confused...
J.delasHeras at ed.ac.uk
- [BioC] bug info
Mathieu Olivier
- [BioC] An error in oligo: All the CEL files must be of the same type??
Setsuko Sahara
- [BioC] DNAcopy
Yan Jiao
- [BioC] heat maps
Brinsmade, Shaun R.
- [BioC] TF database
Ed
- [BioC] limit the number of rows in decideTests
Wendy Qiao
- [BioC] edgeR: Identifying genes up regulated in one of multiple samples, and those stable across samples
Dennis Gascoigne
- [BioC] range data aggregate error
Skirmantas Kriaucionis
- [BioC] edgeR
puvan001 at umn.edu
- [BioC] Questions on doing EdgeR Analysis of Timeseries Data
Gordon K Smyth
- [BioC] about HTqPCR
Heidi Dvinge
- [BioC] colors in plotCtCategory heatmap
Heidi Dvinge
- [BioC] GenomicFeatures more detail.
Fabrice Tourre
- [BioC] edgeR: Identifying genes up regulated in one of multilple samples, and those stable across rsamples
Gordon K Smyth
- [BioC] convert GGtools object (generated by vcf2sm) to snpMatrix class or other class
Mao Jianfeng
- [BioC] methylated and unmethylated function
Zhifu Sun
- [BioC] bug report/repair in vcf2sm of GGtools
Vincent Carey
- [BioC] merging two DNAStringsets
Ullrich, Kristian
- [BioC] DESeq -padj
Dawei Li
- [BioC] fold change after gcrma()
yotsawat pomyen
- [BioC] cause 'memory not mapped'
Won Cheol Yim
- [BioC] analyse GSM files form GEO repository
nac
- [BioC] CEL files not valid?
array chip
- [BioC] Pre-filtering and the gene universe of gene set tests in microarray analysis
François Lefebvre
- [BioC] help with ACME package
Sean Davis
- [BioC] IRanges question!
Asma rabe
- [BioC] ChIPpeakAnno
Zhu, Lihua (Julie)
- [BioC] using and combining of "subseq"
Kristian Ullrich
- [BioC] illumina beadarray GEO files
Nathalie Conte
- [BioC] how to find kinases and their phosphorylating target
Ed
- [BioC] pdmClass plot error
Dick Beyer
- [BioC] rma vs. call.exprs
Assa Yeroslaviz
- [BioC] cluster genes based on expression pattern
Asma rabe
- [BioC] Limma : post statistical gene filtering
Stephanie PIERSON
- [BioC] Biostats/Bioinformatics job University of Washington
Dick Beyer
- [BioC] LIMMAing normalized and background corrected MA-data derived by a text file
"Gläßer, Christine"
- [BioC] flowQ library loading error
René Dreos
- [BioC] converting data matrix to Affybatch object
Pavel Goldstein
- [BioC] Simple, free way to read & assemble ABI sequence data in batch mode?
David Borhani
- [BioC] median normalization in limma
samane fazeli
- [BioC] MA plots for single channel agilent array data, plotMA3by2 and atomic vectors issue
Richard Green
- [BioC] how to make an MA plot with single color agilent microarray?
Richard Green
- [BioC] EdgeR: ANOVA-like analysis
Christian M. Probst
- [BioC] analysis of reference design with even dye-swap across biological replicates
Aubin-Horth Nadia
- [BioC] Using pdInfoBuilder for Human Exon Array
Maria Rodrigo-Domingo / Region Nordjylland
- [BioC] BioC2011 - registration reminder
Valerie Obenchain
- [BioC] Re-annotation of probes for an Affy custom microarray
Ariel Grostern
- [BioC] Help with the weaver example from limma package
Marcus Nunes
- [BioC] Working with Agilent 4X44k array,two color experiment
Srikanth Manda Srinivas
- [BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Virginia Garcia
- [BioC] info on vennCounts function
Alberto Goldoni
- [BioC] Rgraphviz plot of bnlearn object with text too big
João Daniel Nunes Duarte
- [BioC] Installation of Bioconductor packages
Robert DeLisle
- [BioC] rsbml installer cannot find ParseMessage.h from libsbml
Jie Bao
- [BioC] Detection p value cut off
khadeeja ismail
- [BioC] frma vectors for mouse 430 2.0
Ariel Chernomoretz
- [BioC] Infinium 450k beta value distribution
maria giulia bacalini
- [BioC] getSeq on a GRangesList
Michael Cho
- [BioC] A circular problem: re-annotation of custom PM only probes
Ariel Grostern
- [BioC] Follow-up: AnnotationDbi and makeProbePackage for PM-only Affy chips
Ariel Grostern
- [BioC] Limma and spot-specific dye effects for an environmental microarray
Ross Chapman
- [BioC] DNAcopy segment() Infinite Loop
Dario Strbenac
- [BioC] input file in limma package
sanchita 0804
- [BioC] Affymetrix Gene Chip Normalization
Bin Ye
- [BioC] scale and quantile normalization methods in limma
samane fazeli
- [BioC] Classification
David martin
- [BioC] HTqPCR
Marco Fabbri
- [BioC] Comparing Two Affymetrix Arrays Question
Abboud, Ramzi
- [BioC] Converting makeProbePackage in AnnotationDbi to permit PM-only arrays
Ariel Grostern
- [BioC] goseq - overrepresented p-values
Gu Mi
- [BioC] ALL package license
Pierre-Yves Chibon
- [BioC] CMA help
Clara Pons
- [BioC] limma design for tech and biol replicate (1 color design)
Florence Combes
- [BioC] Selecting genes for machine learning
January Weiner
- [BioC] biomaRt package: problem with useDataset() function
Coghlan, Avril
- [BioC] choice of biomaRt feature from annotatePeakInBatch
Zhu, Lihua (Julie)
- [BioC] question about the read.columns
Changbin Du
- [BioC] creating an MA plot with two single channel agilent arrays
Richard Green
- [BioC] limma design for tech and biol replicates (1 color design)
Gordon K Smyth
- [BioC] Subject: Re: Comparing Two Affymetrix Arrays Question
Swapna Menon
- [BioC] RdbiPgSQL regex escape
Håvard Wahl Kongsgård
- [BioC] Package: genomes - update(lproks)
Shinichi Sunagawa
- [BioC] cosine similarity
joe j
- [BioC] Plotting heat map for selected Genes
Srikanth Manda Srinivas
- [BioC] goseq - overrepresented p-values (Alicia Oshlack)
Gu Mi
- [BioC] Information needed for ChIPpeakAnno package
Zhu, Lihua (Julie)
- [BioC] DESeq - fitNbinomGLMs - Error: NA/NaN/Inf in foreign function call
Filippis, Ioannis
- [BioC] Rgraphviz and margins
Robert Stojnic
- [BioC] [OT][job opening]
Tobias Verbeke
- [BioC] error LiWongRank in RNAither
Li, Ning (NIH/NIAID) [F]
- [BioC] biobase
tulay akal
- [BioC] 2 way anova in Bioconductor
Dana.Stanley at csiro.au
- [BioC] AnnotationDbi:makeProbePackage for PM-only chips....getting closer.....now error in installation of probe package
Ariel Grostern
- [BioC] siggenes parameters
Assa Yeroslaviz
- [BioC] [R] help required for GO Annotation problem
Iain Gallagher
- [BioC] Bioconductor Digest, Vol 100, Issue 28
Dennis.Burian at faa.gov
- [BioC] Hypergeometric test in ChIPpeakAnno
Zhu, Lihua (Julie)
- [BioC] IRanges: Request for a "step" argument in runsum
Hervé Pagès
- [BioC] altcdfenvs: mapping probes and creating new probe sets: guidance requested
Ariel Grostern
- [BioC] please remove my address from mailing list
Bea Yu
- [BioC] Retrieving a subset from normalized microarray data for
Gerry S
- [BioC] R crashes with GEOmetadb
Hooiveld, Guido
- [BioC] ChIPpeakAnno package - filter annotatedPeak for GO enrichment analysis
Zhu, Lihua (Julie)
- [BioC] Resend: altcdfenvs: mapping probes and creating new probe sets: guidance requested
Ariel Grostern
- [BioC] negative correlation?
Naomi Altman
- [BioC] limma design and contrast matrices for two-color (two-channel) data with common biological reference, not common mRNA reference
Chris Lasher
- [BioC] sequential removeBatchEffect()?
Jenny Drnevich
- [BioC] rtracklayer Rle to bigWig (export.bw ?)
Arnaud Amzallag
- [BioC] mirna20.db
Ed Siefker
- [BioC] snpMatrix trouble with read.HapMap.data() and ld.snp()
rna seq
- [BioC] dCHip
Ayse Ulgen
- [BioC] Segmentation fault using pair.result.ld.snp in snpMatrix package
rna seq
- [BioC] linear model and continous variable
Dimitris Kampas
Last message date:
Thu Jun 30 22:12:29 CEST 2011
Archived on: Thu Jun 30 22:12:45 CEST 2011
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