June 2014 Archives by thread
Starting: Sun Jun 1 02:36:04 CEST 2014
Ending: Mon Jun 30 22:47:49 CEST 2014
Messages: 457
- [BioC] GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)
Luo Weijun
- [BioC] Warning message while trying to install Bioconductor
Wolfgang Huber
- [BioC] BioC AMI --instance type
Rohmatul Fajriyah
- [BioC] p-values from robust linear model in LIMMA
Arvid Sondén
- [BioC] ChIP-Seq Normalization of mutant vs. WT libraries
Minerva Trejo
- [BioC] PostDoc opportunity
Marc Hild [guest]
- [BioC] Venn diagram with 7 sets
Alpesh Querer
- [BioC] GenomicAlignments and QNAME collision
Valerie Obenchain
- [BioC] SNP ID mapping with oligo package (pd.genomewidesnp.6)
Solip Park
- [BioC] SNP ID mapping with Oligo package
Solip [guest]
- [BioC] makecdfenv package bug
James W. MacDonald
- [BioC] DEXSeqDataSetFromHTSeq Error
Attila [guest]
- [BioC] crlmm : copy number and genotyping of Illumina data
Abhishek Pratap
- [BioC] ECCB 2014
Wolfgang Raffelsberger
- [BioC] GRanges - coercion from dataframe
Ghost
- [BioC] DESeq2 Error in estimateSizeFactorsForMatrix
Caleb Bostwick
- [BioC] compiler error: Rbowtie
Romz34 [guest]
- [BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
Abhishek Pratap
- [BioC] Gviz Incorrect Labels on Features
Lance Parsons
- [BioC] loessByCluster returning error in smooth function in bumphunter
Jiayi Sun
- [BioC] edgeR case-study, SAGE profiles of tumor tissue - where to find data sets?
Lisette de Pillis
- [BioC] Creating a package
Matthew Robert Paul
- [BioC] Transcript clusters missing from hugene20sttranscriptcluster.db
Cornwell, Adam
- [BioC] GAGE RNA-Seq analysis for for a fungi species cryptococcus_neoformans
Luo Weijun
- [BioC] Differences between limma voom E values and edgeR cpm values?
Gordon K Smyth
- [BioC] Rbowtie - compilation error
Romain [guest]
- [BioC] Behaviour of weights in limma
Paul Harrison
- [BioC] DESeq2 - paired sample, interaction and fold change
samuel collombet
- [BioC] Affymetrix HuGene 2.0 ST annotation
Natasha [guest]
- [BioC] install previous version of DEXSeq (1.6.0)
Hatice [guest]
- [BioC] Incorrect result in edgeR.calculateCommonDispersion
Jacob Silterra
- [BioC] Could you help us about DiffBind
Rory Stark
- [BioC] ParseMetaFromGtfFile is.na() error
Beth Wilmot [guest]
- [BioC] SRAmetadb Bioconductor package; study record count low for 2013
Al-Nasir, Jamie (2012)
- [BioC] Worker count specification in functions using bplapply from the BiocParallel pkg
Jerry Davison [guest]
- [BioC] question about flowCore dependencies
Mike
- [BioC] epivizr: Input data type for heatmap
Julian Gehring
- [BioC] GenomicRanges: removing contained ranges without merging overlapping ranges
Jonathan Ellis
- [BioC] Custom GeneSetCollection PFAM
Fabian Grammes
- [BioC] annotations for arrays
Miki Blumenberg [guest]
- [BioC] ComBat() -- run with one sample in one batch
Guest [guest]
- [BioC] Approaches to building Rle sequences from ranges
Vince S. Buffalo
- [BioC] Thread safety of BSgenome getSeq()
Johnston, Jeffrey
- [BioC] topGO genes associated with GO terms
Agnieszka Golicz [guest]
- [BioC] affyxparser -- updating header information
Stacy Hung
- [BioC] Error when applying ComBat in SCAN.UPC
Joel Ma
- [BioC] Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
张超
- [BioC] Issues about how to use rma and paCalls to filter probe sets together
张超
- [BioC] Fwd: limma modeling, paired samples
Riba Michela
- [BioC] VCF class: different length when unlisting INFO CompressedCharacterList
Sigve Nakken
- [BioC] GenomicRanges select parameter
Michael Lawrence
- [BioC] ComBat
Johnson, William Evan
- [BioC] BioC2014 travel scholarship deadline June 10
Martin Morgan
- [BioC] Limma package and minimal number of genes
Bas van Gestel
- [BioC] Installing Workflows for Oligonucleotide arrays
Rinaldy K [guest]
- [BioC] dba.counts error
Ravi Karra
- [BioC] DESeq: Hypothesis testing in multifactor design
yanzhu [guest]
- [BioC] Using DESeq2: experimental design and extracting results
Sridhar A Malkaram
- [BioC] Deseq for pairwise comparison among many pairs
Feng, Shihai
- [BioC] error: 'BiocInstaller' package not in repository
Vrakj [guest]
- [BioC] GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
Janet Young
- [BioC] second GenomicRanges request - enable query-self comparison (and so ignoreSelf and ignoreRedundant) for GRangesList objects?
Janet Young
- [BioC] smoothing function in bumphunter in minfi
Kasper Daniel Hansen
- [BioC] Query regarding SomatiSignature bioconductor package
Anand [guest]
- [BioC] question about how to understand exon usage coefficient value
Alejandro Reyes
- [BioC] DESeq2 new error coming up
Marko Laakso
- [BioC] error writing empty character string in rhdf5 >= 2.8.0
Brad Friedman
- [BioC] Gviz: Plotting mean & CI for DataTrack
Shraddha Pai
- [BioC] Duplicate probe coordinates with pd.hugene.2.1.st and oligo
Steve Piccolo
- [BioC] VariantFiltering: Installation segfault
Julian Gehring
- [BioC] error in subsetting GeneFeatureSet with Oligo
Bruno [guest]
- [BioC] HTqPCR package data layout - how flexible is it?
Ruben Alvarez [guest]
- [BioC] edgeR and DESeq2: model design and estimation of dispersion
Iddo Ben-dov
- [BioC] readDGE
Chinh Hoan
- [BioC] Question flowViz
Mike
- [BioC] Error installing impute package
Levi Waldron
- [BioC] readGappedAlignments not working in Rsamtools
Alvaro [guest]
- [BioC] xy-plot of fcs fails: undefined column selected
Tobias Timmel [guest]
- [BioC] mutant allele read counts
Murli [guest]
- [BioC] problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Blanchette, Marco
- [BioC] Opening Data for NormqPCR (readqPCR)
Camille [guest]
- [BioC] virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Mick Elliot [guest]
- [BioC] DESeq analysis of resistance data
Dave Wettmann [guest]
- [BioC] Installation issue with package GenomicRanges_1.17.18.tar.gz
Minita Shah
- [BioC] Genomic Features - makeTranscriptDbFromGFF()
Geoffrey Thomson [guest]
- [BioC] GLM in EdgeR
Smith H.
- [BioC] non specific filtering 27k methlylation chip
Ninni Nahm [guest]
- [BioC] DiffBind, dba.count result object
Rory Stark
- [BioC] Practical Workshop on High-Throughput Sequencing Data Analysis. 6-10 Oct 2014, OIST, Okinawa, Japan
Gabriella Rustici
- [BioC] crlmm of other software for oncoscan
Richard Friedman
- [BioC] Possible problem with featureCounts() and scipen
Oscar Rueda
- [BioC] wilcox.test error
Nikul Soni
- [BioC] Creating DataFrame uses too much memory
Ludo Pagie
- [BioC] readGAlignmentPairsFromBam with yieldSize & which
Stefano Calza
- [BioC] DNAStringSet_translate error in predictCoding()
"Dr. Jörg Linde"
- [BioC] GenomicFeatures Transcripts Retrieval Fails
Sharvari.Gujja at sanofi.com
- [BioC] Contrast among a subset of interactions, glm in edgeR
Maximo Rivarola
- [BioC] Can my problem be addressed with Bioconductor?
Michela Leonardi [guest]
- [BioC] error on detecting regions
guest [guest]
- [BioC] Error in Views method c()
Michael Dondrup
- [BioC] Elementwise appending of List elements?
Ryan C. Thompson
- [BioC] singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
Hervé Pagès
- [BioC] [DIFFBIND] batch effects and blocking factors
Giuseppe Gallone
- [BioC] EB Seq conditions
Sabet, Julia A
- [BioC] GRanges apply functions
Francesco Lescai
- [BioC] total count filter cutoff (edgeR)
Daniel
- [BioC] ECCB workshop call for abstracts: "Analysis of Differential Isoform Usage by RNA-seq: Statistical Methodologies and Open Software"
Wolfgang Huber
- [BioC] Flowcore - read.FCS : findOffsets problem??
Gaël kaneko
- [BioC] Error in validObject(.Object)
Surles, Monique
- [BioC] ComBat --- Got it working for some variables but not others?!
Celine Bourdon
- [BioC] OpenCyto
Mike
- [BioC] flowClean
Kipper Fletez-Brant
- [BioC] WGCNA_ problem in creating scale free topology plot
amit kumar subudhi
- [BioC] cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Gordon K Smyth
- [BioC] Annotation files for bacterial genome RNAseq
José Luis Lavín
- [BioC] converting probeset id to gene id's : fRMA
Abhishek Pratap
- [BioC] Types of overlap Iranges
Michael Lawrence
- [BioC] Problem with removing duplicated probes of datasets without annotation
Kaj Chokeshaiusaha [guest]
- [BioC] Problom in performing Gene Set Test using KEGG
Aditya [guest]
- [BioC] Complex between and within sample design
Tobias Neumann [guest]
- [BioC] FYI: SCAN.UPC and HuGene 1/2 arrays
Steve Piccolo
- [BioC] Subject: Re: [DIFFBIND] batch effects and blocking factors
Rory Stark
- [BioC] limma lmFit warnings
Nikul Soni
- [BioC] Dates in DataFrames printed incorrectly?
Ryan C. Thompson
- [BioC] VSN with spike-in probes question
Thornton, Matthew
- [BioC] External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
Thornton, Matthew
- [BioC] ConnectivityMap Package (instances, rankMatrix data)
Azam
- [BioC] EasyqPCR package - extracting Standard error values
Tommaso Raffaello
- [BioC] GO enrichment analysis for rice genes
Yong Li
- [BioC] rtracklayer browserView
Dave Gerrard
- [BioC] biomaRt: getSequence returns "Sequence unavailable" where I'd expect NA
Jan Kim
- [BioC] apply function on genomicsRanges obj
gregory voisin
- [BioC] rhdf5 read/write concurrency surprise
Brad Friedman
- [BioC] DESeq2 : Using Normalised ReadCount matrix from EDAseq in DESeq2
Aditi [guest]
- [BioC] apply function on genomicsRanges ob
Greg VOISIN [guest]
- [BioC] create the expression set
guest [guest]
- [BioC] justRMA couldn't obtain CDF environment
Li Liu
- [BioC] DESeqs two-factor two-level, interaction is interested
Shucong Li
- [BioC] Renaming the seqlevels in a transcript database from GenomicFeatures
Fong Chun Chan
- [BioC] merge error: 'by.x' and 'by.y' specify different numbers of columns
Tran, Nhu Quynh T
- [BioC] how to remove probeset
Quan [guest]
- [BioC] biomaRt proxy issues
Enrico Ferrero
- [BioC] SCAN.UPC for microarray and RNAseq data
shirley zhang
- [BioC] No significant p-values
Dave Wettmann [guest]
- [BioC] biomaRt timeout solution?
Xiaokuan Wei
- [BioC] Fwd: Guide vers la personne responsable de "read.FCS"?
Mike
- [BioC] loading qvalue library causes R to abort
Kim S [guest]
- [BioC] Error in Data.frame for mogene10stv1cdf and mogene10sttranscriptcluster.db
Joel Ma
- [BioC] segfault in rqubic
Zhang, Jitao David
- [BioC] FACS Diva Experiment files import
Pierre-Emmanuel Jouve
- [BioC] WGCNA_ Eigengene and sample complications correlations
amit kumar subudhi
- [BioC] specifying continuous independent variables in DESeq2
Jorge Zamora
- [BioC] GenomicAlignments - Speeding up readGAlignmentPairs()
Fong Chun Chan
Last message date:
Mon Jun 30 22:47:49 CEST 2014
Archived on: Tue Jul 1 18:46:21 CEST 2014
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