March 2012 Archives by thread
Starting: Thu Mar 1 00:46:17 CET 2012
Ending: Sat Mar 31 17:04:59 CEST 2012
Messages: 777
- [BioC] cutoff for NUSE plot in oligo
Richard Friedman
- [BioC] adding factors to a data frame from a dataframe
Tom Keller
- [BioC] problem creating own org.Ss.eg.db
Marc Carlson
- [BioC] how to get gene list for given GO terms?
Marc Carlson
- [BioC] how edgeR control outliers?
Yuan Tian
- [BioC] Filtering genes on highest expression before or after LIMMA?
Ekta Jain
- [BioC] Use probesets with highest baseline expression for differntial gene
Ekta Jain
- [BioC] Fw: Warning of function "ncbiTaxonomy"
wuchunyan
- [BioC] PostForm() with KEGG
Ovokeraye Achinike-Oduaran
- [BioC] BiomaRt error: server down?
Lisa Hopcroft
- [BioC] summarizeOverlaps vs countOverlaps
swaraj basu
- [BioC] arrayQualityMetrics error with MAList
karen power
- [BioC] easyRNASeq error
Nicolas Delhomme
- [BioC] IlluminaMousev2.db probe quality information questions?
Mark Dunning
- [BioC] How to include external applications in package vignette code?
Dave Gerrard [guest]
- [BioC] ChIPpeakAnno: Inquiry for Worm Analysis
Zhu, Lihua (Julie)
- [BioC] edgeR: tag vs abundance plot
Alpesh Querer
- [BioC] A problem about trimLRPatterns
wang peter
- [BioC] Finding coding SNPs with predictCoding
Valerie Obenchain
- [BioC] countOverlaps within Mode Counting
Valerie Obenchain
- [BioC] reading with lumi
Tim Triche, Jr.
- [BioC] how to make line graph
Dana.Stanley at csiro.au
- [BioC] GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa
Javerjung Sandhu
- [BioC] Help with plot comparison
Tina Asante Boahene
- [BioC] GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
Javerjung Sandhu
- [BioC] Difficulty in AnnotatedDataFrame
Deepak Datta
- [BioC] Provide an Example for AnnotatedDataFrame
Deepak Datta
- [BioC] Biobase typo in example of AnnotatedDataFrame man page
James F. Reid
- [BioC] Summarizing Single-channel Agilent data
David Westergaard
- [BioC] Gene-Metabolite correlation network
pankaj borah
- [BioC] KEGGSOAP
Ricardo Silva
- [BioC] GAGE heatmap pdf question...
Alan Derr
- [BioC] unable to readImage using EBImage package
diyanah [guest]
- [BioC] beadarray vignette has broken code in R2.14.1?
Dan Tenenbaum
- [BioC] arrayQualityMetrics package - bugs and errors
Wolfgang Huber
- [BioC] report a possible bug of
Martin Morgan
- [BioC] impute.knn
Ali Mohammadian
- [BioC] cannot allocate vector for random forest
Salwa Eid
- [BioC] FrozenRMA how to
Alejandro Sánchez Pla
- [BioC] can't allocate vector for random forest
Salwa Eid
- [BioC] arrayQualityMetrics error and question
David Westergaard
- [BioC] normalize.invariantset
Ali Mohammadian
- [BioC] GSVA with entrez ids?
Ed Siefker
- [BioC] re incomplete analysis in Deseq
Julian [guest]
- [BioC] error using random forest
Salwa Eid
- [BioC] how to rank affy probesets by their probe-effect magnitude
Robert Castelo
- [BioC] "charm" for MeDIP?
Johnny
- [BioC] ggplot2: changing the axes appearance
Faryabi, Robert (NIH/NCI) [F]
- [BioC] aCGH segmentation with DNAcopy
Emilie Lalonde
- [BioC] limma package topTable error
Monica Wong
- [BioC] ChIPpeakAnno as.data.frame error
Mark Cowley
- [BioC] Gviz question
Hahne, Florian
- [BioC] AnnotationDbi - makeOrgPackageFromNCBI - gene_info table is not populated
Jiri Voller [guest]
- [BioC] Checking RNAseq DESeq pipeline
nathalie
- [BioC] error in using random forest
Salwa Eid
- [BioC] EBImage: Negative pixel intensities?!?
Henrik Bengtsson
- [BioC] Any code for simulation of qPCR studies?
Ali Mohammadian
- [BioC] clusterCt {HTqPCR}
Ali Mohammadian
- [BioC] File formats for high throughput qPCR data
Heidi Dvinge
- [BioC] fastest way to get a gene list having certain GO term
Duke
- [BioC] homopolymer gap extension penalty in Biostrings
Hervé Pagès
- [BioC] classify SNPs
Kunbin Qu
- [BioC] fisher exact test pairwise comparisons
Alyaa Mahmoud
- [BioC] plotting a CA
aoife [guest]
- [BioC] RobustSpline normalization method applied to agilent data
Priscila Grynberg
- [BioC] creating GRanges and reading BAM files
David A.
- [BioC] Problem with Bimap objects
Lola Guerrero
- [BioC] snpStats, read.long, alleles in two columns
Liz Hare
- [BioC] Problem fitting a linear model using limma
Joaquin Martinez
- [BioC] question about biomaRt problem
rong [guest]
- [BioC] svm (e1071) class weighting in a multi-class problem
Javier Pérez Florido
- [BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"
henlen [guest]
- [BioC] batch effect confounded with condition
tefina
- [BioC] chi-squared
Aaral [guest]
- [BioC] A few Q's on using DEXSeq with mucho data
Steve Lianoglou
- [BioC] Problem installing GenomicFeatures
Georg Otto
- [BioC] makeOrgPackageFromNCBI another error - reversed commands
Jiri Voller [guest]
- [BioC] how to read empty line in the fastqfile
wang peter
- [BioC] a possible bug of trimLRPatterns
wang peter
- [BioC] Question about Normalization
James [guest]
- [BioC] error of justRMA() under Linux
cao zongfu
- [BioC] for running arrayQualityMetrics
Benilton Carvalho
- [BioC] Error by using gpr data with marray
Sandra Heise [guest]
- [BioC] How to combine different annotation (chromosomic, genic) when using easyRNASeq (was easyRNASeq error)
Nicolas Delhomme
- [BioC] how can i apply random forest to expression sets of dna microarray
Salwa Eid
- [BioC] Coverage Question: GenomicRanges
Lakshmanan Iyer
- [BioC] a problem with trimLRPatterns
wang peter
- [BioC] LIMMA - summarization
Kripa R
- [BioC] Need immediate help please-BeadSummaryData
Cute Guy
- [BioC] plotting a ca.
Aaral Singh
- [BioC] error in locateVariants for a GRanges object
Lescai, Francesco
- [BioC] Z-scores
Alyaa Mahmoud
- [BioC] ChipPeakAnno question about file conversion
Zhu, Lihua (Julie)
- [BioC] LIMMA - summarization of Illumina probes for same gene
Gordon K Smyth
- [BioC] question from any of TopGO, gage, sigpathway, GSVA, GOstat users
Ali Mohammadian
- [BioC] edgeR i get 377 significant genes where in DESeq i got 0
papori [guest]
- [BioC] Intersecting two chromosomal ranges but keeping the unique ones
Yadav Sapkota
- [BioC] can't get degree function to work in graph package
Burak Kutlu
- [BioC] question about makeVennDiagram
Zhu, Lihua (Julie)
- [BioC] Newer version of DESeq give much small list of DE genes
Creasy, Todd
- [BioC] EBImage in R-Cloud
Nicole [guest]
- [BioC] limma multiple groups comparison produces different pvalue comparing with two group comparsion
Shao, Chunxuan
- [BioC] Error in reading 450k data using lumiMethyR
khadeeja ismail
- [BioC] Pre-filtering before differential expression analysis in LIMMA
Karthik K N
- [BioC] Ensembl gene ids corresponding to affymetrix rat exon array transcript level ids
James Perkins
- [BioC] LumiT VST error
Paolo Kunderfranco
- [BioC] (no subject)
James Perkins
- [BioC] breastCancerMAINZ package installation problem
Coghlan, Avril
- [BioC] survival prediction from multiple genes
Ahmet ZEHIR
- [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
Hervé Pagès
- [BioC] pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays
Groot, Philip de
- [BioC] cummeRbund package function diffData returns no rows for TSS features
Asta Laiho [guest]
- [BioC] R course: London, Monday 18th - Friday 22nd June 2012.
Leo Schalkwyk [guest]
- [BioC] DESeq without replicates, Problem trying to obtain significant hits
Melissa.Martin at lshtm.ac.uk
- [BioC] Bioconductor Digest, Vol 109, Issue 14
Pan Du
- [BioC] DNA sequence analysis question
andigoni
- [BioC] setting up the correlation matrix with two channel, dye swapped data . How to deal with Bio and Tech replicates?
Richard Green
- [BioC] a way to select and filter edge attributes in RCytoscape
Burak Kutlu
- [BioC] how to get pig genome and for miRNA target scan
wang peter
- [BioC] annotate htmlpage error
Georg Otto
- [BioC] Ensembl and refseq genes
chris Jhon
- [BioC] problems using the latest version of e1071 (svm)
Javier Pérez Florido
- [BioC] How to choose the most 2 different samples in an array experiment
Ali Mohammadian
- [BioC] Question about hgu133plus2cdf?
Fabrice Tourre
- [BioC] Limma and negative p-values
Ovokeraye Achinike-Oduaran
- [BioC] New to Bioconductor is there a better way?
Davis, Brian
- [BioC] ChIPpeakAnno on pathway enrichment
Zhu, Lihua (Julie)
- [BioC] ChIPpeakAnno: makeVennDiagram and sampling peaks
Zhu, Lihua (Julie)
- [BioC] 13th MRC Social, Genetic & Developmental Psychiatry SUMMER SCHOOL 18th - 22th June 2012
Ramasamy, Adaikalavan
- [BioC] Please help : RGraphviz installation problem version 1.32 in Ubuntu and Windows 7
Amit Kumar Kashyap
- [BioC] extracting sequence from a genome
Iain Gallagher
- [BioC] World's biggest fake conference in computer science
James Allen
- [BioC] Question about limma package
Anna Dvorkin
- [BioC] Job Announcement: Genome Informatics
Zadeh, Jenny Drnevich
- [BioC] 2 more Job Announcements
Zadeh, Jenny Drnevich
- [BioC] Alert to developers about changes to edgeR
Gordon K Smyth
- [BioC] RCytoscape not recognizing initiated edge attributes.
Burak Kutlu
- [BioC] IRAnges compile error
Francoise.LECOMTE at biogemma.com
- [BioC] optimizing class weights in e1071
Javier Pérez Florido
- [BioC] edgeR-How to obtain a list of normalized expression values
Philipp Brand
- [BioC] an error from ShortRead
wang peter
- [BioC] readGappedAlignments, package:GenomicRanges
Milica Krunic
- [BioC] question regarding ChIPPeakAnno use
Zhu, Lihua (Julie)
- [BioC] rsbml: problem writing a model to file
hettling
- [BioC] post-doctoral position
Day, Roger S
- [BioC] any good R package to scan microRNA target?
wang peter
- [BioC] an erro related with RNAStringSet
wang peter
- [BioC] Copy number analysis
Raj [guest]
- [BioC] cummeRbund loading error
SC [guest]
- [BioC] making use of the Apis mellifera BeeBase assembly 4 data in goseq
Matthew Young
- [BioC] Copy Number Analysis for Mapreduce
My Coyne
- [BioC] edgeR MDS plot
Lina Weber
- [BioC] problem getting setNodeColorRule from RCytoscape to work
Burak Kutlu
- [BioC] A question about MA and RG lists and normalization with two channel agilent arrays.
Richard Green
- [BioC] how to map Affymetrix ID to ensemble gene ID
wang peter
- [BioC] how to write fasta file of RNA sequences
wang peter
- [BioC] biomaRt cannot find getAffyArrays function
wang peter
- [BioC] Affymetrix Intronic Normalization Control Probes Differentially Expressed?
Alexandra Muñoz
- [BioC] Rgraphiz
zahra / زهرا ghayyomi / قیومی
- [BioC] biocLite() does not accept 'lib.loc' for updating
Martin Maechler
- [BioC] NOISeq-real input parameters
papori [guest]
- [BioC] qcplot() error in methylumi?
Oliver Lyttleton
- [BioC] JOB: Research Associate in Statistical Epigenomics (London)
Andrew Teschendorff
- [BioC] SNP Frequency Analysis Package in Bioconductor
Javerjung Sandhu
- [BioC] design and contrast matrix for limma time series without replicates
Chunxuan Shao
- [BioC] getGEO and wilcox.test
Ovokeraye Achinike-Oduaran
- [BioC] Manually upregulate a gene
Reema Singh
- [BioC] Chairman disappears from world's biggest computer conference
James Allen
- [BioC] Problems using arrayQualityMetrics
Rosalind Cutts
- [BioC] Summing Views on coverage by base
Sean Davis
- [BioC] DESeq Question
Omar Darwish
- [BioC] Is the qrqc package source updated?
NDowell
- [BioC] DESeq multi-factor export results
Ingrid Lindquist
- [BioC] problems generating a gene2GOlist in topGO
António Miguel de Jesus Domingues
- [BioC] Duplicate probes
Ed Siefker
- [BioC] DeSeq Volcano plot- error
Melissa.Martin at lshtm.ac.uk
- [BioC] BioMart server down yesterday and today? Error
Adriana Munoz
- [BioC] eset from GEOqury pkg
Jing Huang
- [BioC] SRAdb error
Ayten YIGITER
- [BioC] How can I access to a gene set
Lola Guerrero
- [BioC] PPDE results with 'NA' for the web Cyber-t
Li Zhang
- [BioC] plot axis in pROC
David martin
- [BioC] Get negative control probes in lumiBarnes data set
Sandra Plancade [guest]
- [BioC] Please help: SNP Frequency Analysis Package in Bioconductor
Javerjung Sandhu
- [BioC] Using Anova for microarray data
konika chawla
- [BioC] ChIPpeakAnno findVennCounts
Zhu, Lihua (Julie)
- [BioC] rtracklayer export.wig variableStep problem
Vincent Schulz
- [BioC] Adjacency to network using R
pankaj borah
- [BioC] Error when using impute to get missing values
David Westergaard
- [BioC] problems installing xcms package
Juliet Hannah
- [BioC] GRENITS won't run with example data
Tyler Funnell
- [BioC] crlmm and Affymetrix SNP5 array [genotyping issues]
Ali ZAIDI
- [BioC] saving GRangesList object; conversion to GFF
Milica Krunic
- [BioC] DESeq vs DEXSeq
Robert M. Flight
- [BioC] DESeq estimateDispersion options for lower depth miRNA-seq
Aggarwal, Praful
- [BioC] curious IRanges error when sort()ing a GRanges
Tim Triche, Jr.
- [BioC] distanceToNearest for GRanges?
Janet Young
- [BioC] Updating Package Versions from SVN
chris_utah
- [BioC] calcNormFactors()
Anand K S Rao
- [BioC] Up & Downregulated genes using DESeq
Omar Darwish
- [BioC] DESeq- figures on variance estimation
Melissa.Martin at lshtm.ac.uk
- [BioC] DESeq for two-factor models
Henning Wildhagen
- [BioC] variance and coefficient of variation with edgeR
Miguel Gallach
- [BioC] Looks like a bug in GenomicRanges::.breakTie
Paul Theodor Pyl
- [BioC] Problems installing EBImage package
Marco Sassi [guest]
- [BioC] beadarray package: BASH error
Kemal Akat [guest]
- [BioC] DESeq estimateDispersion options for lower depth
Aggarwal, Praful
- [BioC] Plot Cumulative graph
Tina Asante Boahene
- [BioC] HTqPCR: normalizeCtData
Ali Mohammadian
- [BioC] dispatch method
Stefanie
- [BioC] running time: countOverlaps & summarizedOverlaps vs. HTSeq
Milica Krunic
- [BioC] edgeR: Specifying the "coef"-argument in glmLRT in a two factor study
Henning Wildhagen
- [BioC] GEOquery Data structure: GSEMatrix
Hendrik Falk
- [BioC] Rsamtools installation
Bruce Hayward
- [BioC] F p.value.adj missing from write.fit/limma
Pascal Gellert
- [BioC] ChIPpeakAnno - Request of information
Zhu, Lihua (Julie)
- [BioC] some questions about lumi package and Illumina arrays
Javier Pérez Florido
- [BioC] oligo package: extracting position, sequence, and intensity from Affymetrix tiling array
Cindy [guest]
- [BioC] RangedData Element Metadata
Dario Strbenac
- [BioC] edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation?
Miguel Gallach
- [BioC] flip strand information in GappedAlignments or GRangesList Object
Stefanie
- [BioC] Rgraphviz and node label placement
Iain Gallagher
- [BioC] LIMMA package - coefficient not estimable
yeeling chong
- [BioC] DNAcopy for CNV in SNP Affy 6.0
Ekta Jain
- [BioC] R is the most popular programming language in Bioinformatics
Michael Barton [guest]
- [BioC] Help with lumi R package
Minyue Wang
- [BioC] edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Gordon K Smyth
- [BioC] fitmaanova
Maxime Deraspe [guest]
- [BioC] Using the untar() with getGEOSuppFiles()
Ovokeraye Achinike-Oduaran
- [BioC] oligonucleotideTransitions from Biostrings package
Muino, Jose
Last message date:
Sat Mar 31 17:04:59 CEST 2012
Archived on: Sat Mar 31 17:05:16 CEST 2012
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