August 2014 Archives by thread
Starting: Fri Aug 1 00:08:31 CEST 2014
Ending: Sun Aug 31 18:33:43 CEST 2014
Messages: 440
- [BioC] "F is dropped because no value found!" error of read.FCS
Mike
- [BioC] chip removal from lumiBatch object
Kilo Morkowi
- [BioC] ANOVA analysis using edgeR
Yogender Gowtham
- [BioC] Question about decideTestsDGE
Gordon K Smyth
- [BioC] DEXSeq continous variable in model
Alex Gutteridge
- [BioC] deepSNV error
Asma rabe
- [BioC] CAGEr - How to change plot axis range in CAGEr
Tobias Hohenauer
- [BioC] DEXSeq: No log2FCs in DEXSeqResult table
Fabian Grammes
- [BioC] Combat: Removing multiple batch effects
Shaun Webb [guest]
- [BioC] Any problem with the design matrix or the contrasts? Thanks
Rao,Xiayu
- [BioC] Steps of removing batch effects and hidden variables
shirley zhang
- [BioC] Microarray data normalization
Levi Waldron
- [BioC] DESeq2 basemean and log2foldchange
rob yang
- [BioC] NuPoP cannot recognize my fasta file
Catherine [guest]
- [BioC] RNA-Seq, generate batch-free count matrix
Steve Lianoglou
- [BioC] Doubts regarding Pathview
Luo Weijun
- [BioC] CRISPRseek: findgRNAs bug?
Zhu, Lihua (Julie)
- [BioC] CRISPRseek: bug, or did I make an error?
Zhu, Lihua (Julie)
- [BioC] CRISPRseek: searchHits() optimization
Zhu, Lihua (Julie)
- [BioC] ChIPpeakAnno for overlapping gene features
Zhu, Lihua (Julie)
- [BioC] multi-level design - a simplified question - corrected table
Gordon K Smyth
- [BioC] "True" normalization factors in edgeR
Zhan Tianyu
- [BioC] spike-in normalization with NormiR
Svetlana Bojic [guest]
- [BioC] CAMERA on Mac OS X 10.9 (Mavericks)
amsha nahid [guest]
- [BioC] CRSIPRseek: no summary file generated
Zhu, Lihua (Julie)
- [BioC] More than one package document with the same name
Jerry Davison [guest]
- [BioC] Error in keggPathwayGraphs when updateCache = TRUE
Shruti Marwaha [guest]
- [BioC] updating edge visualization rules of an existing graph in RedeR
burak kutlu
- [BioC] warning with lmFit command in limma
Shruti Marwaha [guest]
- [BioC] removeBatchEffect options: design and covariates
Rao,Xiayu
- [BioC] Contrast matrix in limma
Ryan C. Thompson
- [BioC] Contrast among a subset of interactions, glm in edgeR
Ryan C. Thompson
- [BioC] edgeR: Analyze mini-time-series MeDIP data of pooled DNAs without replicates?
Vang Quy Le / Region Nordjylland
- [BioC] Error in DESeqDataSetFromHTSeqCount: scan line did not have 2 elements
Jon Bråte
- [BioC] finding differential expression pattern between paired columns of data frame.
Jakub Stanislaw Nowak
- [BioC] Question regarding the use of the snapCGH package to analyze aCGH data obtained from TCGA
Ajay Singhal [guest]
- [BioC] plotIdeogram for non-human or mouse genome
Mark Dunning
- [BioC] Can DESeq do this?
Pet Chiang
- [BioC] bug in graph::removeEdge() on UGs with graphBAM objects
Robert Castelo
- [BioC] question about Gviz
Hahne, Florian
- [BioC] Gviz: Plotting mean & CI for DataTrack
Hahne, Florian
- [BioC] Useful information about Ensembl release 76 mart databases
Thomas Maurel
- [BioC] Package oligo: Transcript level P/A calls
Mukund, Kavitha
- [BioC] gpQuality Error
Edra [guest]
- [BioC] circlize package: some error message
Fix Ace
- [BioC] edgeR: Analyze mini-time-series MeDIP data of pooled DNAs without replicates
Gordon K Smyth
- [BioC] deseq2: convert ensembl ID to gene symbol.
Fabrice Tourre
- [BioC] iranges
carol white
- [BioC] Generating heat map of pre-organised data in matrix without clustering using ggplot2 or heatmap.2
Jakub Stanislaw Nowak
- [BioC] Reading by column
pep
- [BioC] ComBat: it.sol error
Anna Christine Reisetter
- [BioC] "Normalising" GRanges coverage object
Aliaksei Holik
- [BioC] False positives due to GC content correction - DESeq2
Aditi [guest]
- [BioC] Can't use package [pd.mapping250k.sty]
Marcelo Pereira
- [BioC] WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Sindre Lee
- [BioC] question about DEXSeq from a count table, stopped at estimateExonFoldChanges
Ou, Jianhong
- [BioC] GO enrichment
Warin [guest]
- [BioC] Deseq2 for down stream analysis
Fabrice Tourre
- [BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
Valerie Obenchain
- [BioC] narrow and xstringset
carol white
- [BioC] ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Zhu, Lihua (Julie)
- [BioC] [OT] Job Openings: Data Analyst and Data Scientist at OpenAnalytics (Belgium)
Tobias Verbeke
- [BioC] problems running DEseq2
Julian Rozenberg [guest]
- [BioC] limma design matrix and contrast specification for time course PCR data with two conditions and variable replicate number
Linus Schumacher
- [BioC] GWASTools: assocTestRegression, forcing the analysis to use reference allele
Danica [guest]
- [BioC] SomaticCancerAlterations:::.validate_maf, read_maf, maf2gr
Aedin Culhane
- [BioC] DESeq: multi-factors testing questions
Yanzhu Lin
- [BioC] deseq2 for pair-wise analysis
Subbaiah Chalivendra [guest]
- [BioC] Issue with flowDensity on OpenCyto
Mike
- [BioC] flowviz
Mike
- [BioC] b37 version of BSGenome for Gviz
mehaffey
- [BioC] Downgrading R to an older version
Chong Kim San Allen
- [BioC] edgeR, very big lib.size makes CPM very small
Vang Quy Le / Region Nordjylland
- [BioC] CRISPRseek question on scoring
Zhu, Lihua (Julie)
- [BioC] Question about ChipPeaksAnno and intersect
Zhu, Lihua (Julie)
- [BioC] GAGE/Pathview analysis data preparation
Luo Weijun
- [BioC] edgeR: Problem with subsetting a DGEList in latest package version
Katja Hebestreit
- [BioC] ChIPpeakAnno 2.12.2 bug
Zhu, Lihua (Julie)
- [BioC] sampleSheet problem in beadArray
Christine Stansberg [guest]
- [BioC] Are the logFC confidence intervals returned by topTable adjusted for multiple comparisons?
Calin-Jageman, Robert
- [BioC] gpQuality and readGPR errors for Microarrays [arrayQuality Package]
Edra [guest]
- [BioC] strange log2FoldChange estimates
Shi, Tao
- [BioC] (no subject)
Gary Meyer
- [BioC] Error while mapping SYMBOLS to ENTREZID
Atul Kakrana
- [BioC] GRanges list and reduce function
Asma rabe
- [BioC] zero rna-seq values AFTER normalisation in edgeR
Nick N
- [BioC] DEXSeq update results change
António domingues
- [BioC] Announcing Bioconductor's youTube Channel
Sonali Arora
- [BioC] Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
Anne Deslattes Mays
- [BioC] Protein position to genomic location
Dave Wettmann [guest]
- [BioC] R package not available for R v3.1.1
CSI [guest]
- [BioC] Why is the volcano plot from limma package is more beautiful ( symmetrical ) than that from raw t.test calculation?
my1stbox
- [BioC] normalization and batch correction across multiple project
Adaikalavan Ramasamy
- [BioC] Genes2GO and suggestions to make it faster
Konika Chawla
- [BioC] Please help us try out our new support site!
Marc Carlson
- [BioC] Extract junction reads from bam
Helen Zhou
- [BioC] ggvis: interactive heatmaps
Abhishek Pratap
- [BioC] Multifactor model design for DE analysis (DESeq2 & edgeR)
Mathieu Bahin
- [BioC] Bioinformatics Analyst opportunity at the University of Cambridge/Cancer Research UK (Permanent, full-time)
Suraj Menon
- [BioC] How to create expression objects with evaluated arguments?
my1stbox
- [BioC] multiple level factors contrast in nbinomLRT, DESeq2.
sh. chunxuan
- [BioC] How "eval" results returned by "paste0" ?
my1stbox
- [BioC] How can I create a variable with name indicated by argument during function run?
my1stbox
- [BioC] DESeq: Hypothesis testing in multifactor design
Yanzhu Lin
- [BioC] ChIPpeakAnno
Zhu, Lihua (Julie)
- [BioC] Filtering pmSequence based on probe target level for HTA 2.0 arrays
Steve Piccolo
- [BioC] Robustspline and two dimentional loess for two color agilent data
Samane [guest]
- [BioC] Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
Scott Robinson [guest]
- [BioC] Taking out a plate from a HTS analysis
Rossella Rispoli [guest]
- [BioC] Plate config for 1536 plate into cellHTS2
Rossella Rispoli [guest]
- [BioC] Model Design
Sander [guest]
- [BioC] ggbio error: Objects of type OrganismDb not supported by autoplot
Georg Otto
- [BioC] nearly exact overlaps between GAlignmentPairs and GenomicRanges
Georg Otto
- [BioC] rsqlite for windows from fhcrc
Kasper Daniel Hansen
- [BioC] pintersect GRanges with empty results
Christian Ruckert
- [BioC] Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip
Gordon K Smyth
- [BioC] Problem in K- means clustering
Aditya Saxena
- [BioC] DESeq
cbpp300 [guest]
- [BioC] subseq with iranges on reverse strand
Hervé Pagès
- [BioC] genefilter installation error
Subinoy Biswas
- [BioC] WGCNA: help with comparing multiple GEO studies
Abhishek Pratap
- [BioC] readRNAMultipleAlignmen - filepath
KoRR [guest]
- [BioC] Interspecies differential expression of orthologs with Edger
assaf www
- [BioC] DESeq2: likelihood ratio test
Quynh Tran
- [BioC] Shearwater question
Asma rabe
- [BioC] Best practices to find intersection among variants
Blanchette, Marco
- [BioC] ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Preussner, Jens
- [BioC] Plotting arbitrary lines at Gviz plotTracks
Vinicius Henrique da Silva
- [BioC] topGO
Steven Stadler
- [BioC] How does MEDIPS handle multiple mapping of a read
Allen [guest]
- [BioC] Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
Guilherme Rocha
- [BioC] Single sample normalization of single-channel Agilent microarrays
Gabriele Zoppoli [guest]
- [BioC] DESeq2 design
Guest [guest]
- [BioC] autoplot() in ggbio package for txdb object
Tengfei Yin
- [BioC] ggbio plot coverage adjusted for library size
Tengfei Yin
- [BioC] Recent course materials now easily searchable
Dan Tenenbaum
- [BioC] Bioconductor Digest, Vol 138, Issue 27
Laurent Gatto
- [BioC] What are the best packages to compare multiple DE gene lists?
Stephane Plaisance | VIB |
- [BioC] Using custom CDF with 'make.cdf.env'
Scott Robinson [guest]
- [BioC] Rsubread featureCounts unexpected strand-specifc counts with Ensembl GTF
Kaur Alasoo [guest]
- [BioC] getting normalized expression values from GEO GSE files
Maria Kesa
- [BioC] heatmap.2: Colv dendrogram doesn't match size of x
ferreirafm at usp.br
- [BioC] edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Nick N
- [BioC] Combing Effects (t-stats) from experiment with common reference design?
Atul
- [BioC] IRanges findOverlaps potential bug?
Arunkumar Srinivasan
- [BioC] hugene10sttranscriptclusterACCNUM has no mappings
Thomas Pfau
- [BioC] parallel BAM sorting with Rsamtools
Jens Reeder [guest]
- [BioC] questions about gage
Luo Weijun
- [BioC] packages similar to Jetset but for mouse platforms
Laurent.Pays
- [BioC] DESeq2: df error message with nbinomial LRTest
INRA - coutellec
- [BioC] Running cufflinks for spliceR
Hanquan Liang
Last message date:
Sun Aug 31 18:33:43 CEST 2014
Archived on: Sun Aug 31 18:34:47 CEST 2014
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