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Beadarray error: comparison of types not implemented
Annotation ExperimentData Cancer Biobase beadarray Annotation ExperimentData Cancer
16.8 years ago Martin Morgan 25k
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1
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1.4k
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justGCRMA problem :(
GO Cancer gcrma matchprobes PROcess affyio GO Cancer gcrma matchprobes PROcess affyio
updated 16.8 years ago by ▴ 20 • written 16.9 years ago by 25k
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Bioinformatics postdoc in Brussels
Sequencing Epigenetics Cancer Breast Sequencing Epigenetics Cancer Breast
16.8 years ago Vincent Detours ▴ 80
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886
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Problems reading single channel GenePix data with read.maimages.
Cancer Cancer
16.8 years ago Martin Morgan 25k
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1
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1.2k
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Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
16.8 years ago Martin Morgan 25k
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13
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4.2k
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GEOmetadb and gse organism type
Cancer Breast Organism GEOmetadb Cancer Breast Organism GEOmetadb
updated 16.8 years ago by 21k • written 16.8 years ago by ▴ 180
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Warning in mergeLevels
aCGH Cancer aCGH aCGH Cancer aCGH
16.8 years ago Oscar Rueda ▴ 40
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675
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script line to multiply a vector by another vector or matrix
Cancer Cancer
16.8 years ago Hervé Pagès 16k
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2.3k
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GEO metadata
Cancer GEOquery GEOmetadb Cancer GEOquery GEOmetadb
16.9 years ago Jack Zhu ▴ 170
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3
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1.3k
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Curious file size issues
Annotation Cancer PROcess Annotation Cancer PROcess
updated 16.9 years ago by 6.7k • written 16.9 years ago by ★ 1.9k
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810
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matchPdict error
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
16.9 years ago Hervé Pagès 16k
0
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3
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1.4k
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Biomart Error
Cancer biomaRt Cancer biomaRt
updated 16.9 years ago by ▴ 660 • written 16.9 years ago by ▴ 40
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Assistant/Associate Professor Department of Biostatistics
Pathways Bayesian Cancer charm Pathways Bayesian Cancer charm
16.9 years ago Kellie J. Archer, Ph.D. ▴ 120
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1.9k
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PhD / PostDoc positions in Innsbruck, Austria
Microarray GO Cancer Leukemia Microarray GO Cancer Leukemia
16.9 years ago Johannes Rainer ▴ 80
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Help: Problems with LmFit
Cancer limma Cancer limma
16.9 years ago julin@aecom.yu.edu ▴ 80
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3
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7.6k
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org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Cancer Homo sapiens convert Cancer Homo sapiens convert
updated 16.9 years ago by ▴ 10 • written 16.9 years ago by ★ 1.1k
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2
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1.5k
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Repost of Error Message: Error in dim(data)<-dim: attempt to set an atrribute on NULL
Cancer PROcess Cancer PROcess
updated 16.9 years ago by 68k • written 16.9 years ago by 25k
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1.7k
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About the bioconductor package SNPlocs.Hsapiens.dbSNP.20071016.
SNP Cancer SNPlocs SNP Cancer SNPlocs
16.9 years ago Hervé Pagès 16k
1
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1
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6.3k
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Limma: Contrasts comparing one factor to multiple others
Cancer limma Cancer limma
updated 16.9 years ago by 68k • written 16.9 years ago by ★ 1.9k
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3
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1.9k
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Gostats with Yeast annotation
Microarray Annotation GO Cancer Yeast GOstats Microarray Annotation GO Cancer Yeast
16.9 years ago Yolande Tra ▴ 160
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1.1k
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Limma contrasts with model.matrix
Microarray Cancer Microarray Cancer
16.9 years ago Daniel Brewer ★ 1.9k
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1.3k
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qPCR 2009 Event Agenda Online
SNP qPCR Normalization Visualization Regression Cancer probe microRNA SNP qPCR Cancer
16.9 years ago qPCR Platform - the reference in real-t… ▴ 170
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1.3k
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[JOB] National Cancer Institute, Bethesda, MD
Sequencing miRNA Microarray Genetics Cancer Sequencing miRNA Microarray Genetics Cancer
17.0 years ago Sean Davis 21k
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2
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1.2k
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read.maimages(limma) source="agilent" updated for 20-bit scanner?
Cancer Cancer
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 30
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2.1k
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getSeq human genomic sequences
Annotation Cancer BSgenome PROcess GLAD BSgenome IRanges Annotation Cancer BSgenome GLAD
17.0 years ago Hervé Pagès 16k
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3
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1.5k
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Limma without eBayes correction
Cancer limma Cancer limma
updated 17.0 years ago by 68k • written 17.0 years ago by ★ 1.9k
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3
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1.7k
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BiomaRt error when trying to get exon location info
Cancer biomaRt Cancer biomaRt
updated 17.0 years ago by ▴ 600 • written 17.0 years ago by ★ 1.9k
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LIMMA Error Message:Error in new("AnnotatedDataFrame", data = phenotypicdata) : trying to generate an object from a virtual class ("AnnotatedDataFram…
Cancer limma Cancer limma
17.0 years ago Martin Morgan 25k
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1.2k
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Adding names to a IRanges object
Cancer IRanges Cancer IRanges
updated 17.0 years ago by ▴ 620 • written 17.0 years ago by ★ 1.9k
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2.0k
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Genome position to miRNA or gene name
miRNA Alignment GO Cancer BSgenome BSgenome miRNA Alignment GO Cancer BSgenome BSgenome
updated 17.0 years ago by 25k • written 17.0 years ago by ★ 1.9k
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full Professor position in bioinformatics in Innsbruck, Austria
Cancer Cancer
17.0 years ago Johannes Rainer ▴ 80
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1.4k
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SAM warning
Biophysics Alignment Annotation Normalization Cancer hgu133plus2 probe affy vsn MBCB vsn
17.0 years ago elliot harrison ▴ 230
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6
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3.6k
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Filtering before differential expression analysis of microarrays - New paper out
Cancer Cancer
updated 17.0 years ago by 53k • written 17.0 years ago by ★ 1.9k
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1.1k
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multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment Annotation Cancer hgu133plus2 probe affy Biostrings Alignment Annotation Cancer
17.0 years ago rgentleman ★ 5.5k
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1.3k
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Luminex Data Analysis
Cancer Cancer
17.0 years ago Samuel Pine ▴ 10
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5.1k
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Error in getClass(Class, where = topenv(parent.frame())) : "AnnotatedDataFrame" is not a defined class
Cancer limma Cancer limma
17.0 years ago Martin Morgan 25k
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1.5k
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NEW deadline - Talk & Poster Call - qPCR 2009 Event
SNP qPCR Normalization Visualization Regression Cancer probe microRNA SNP qPCR Cancer
17.0 years ago qPCR Platform - the reference in real-t… ▴ 170
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935
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how can I apply a function to each element of a GeneSetCollection (GSEABase)
Cancer Cancer
17.0 years ago Martin Morgan 25k
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1
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1.7k
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Talk & Poster - Final Call - qPCR 2009 Event
SNP qPCR Normalization Visualization Regression Cancer probe PROcess microRNA SNP qPCR
17.1 years ago qPCR Platform - the reference in real-t… ▴ 170
0
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769
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Question about graph package
Cancer graph Rgraphviz Cancer graph Rgraphviz
17.1 years ago Florian Hahne ▴ 540
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1.6k
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sd==0 for some probesets when using gcrma
Microarray Proteomics Epigenetics Normalization GO Cancer hgu95av2 affy graph gcrma GO
17.1 years ago Dick Beyer ★ 1.4k
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989
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Detecting mRNA Expression When Somatic Mutations Have
Microarray Cancer Microarray Cancer
17.1 years ago Alicia Oshlack ▴ 70
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1.1k
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Cannot Subset Columns in beadarray package, ExpressionSetIllumina Class in R-2.8.0, BioBase 2.2.1, beadarray 1.10.0
Cancer beadarray Cancer beadarray
17.1 years ago Julian Lee ▴ 140
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831
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Problem of combine function when combining different numeric types
Cancer convert Cancer convert
17.1 years ago Martin Morgan 25k
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873
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Colourful way of visualising differential analysis results
Microarray Cancer limma Microarray Cancer limma
17.1 years ago Yannick Wurm ▴ 220
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2.3k
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[R] BioC 2.3 standard installation
Cancer preprocessCore Cancer preprocessCore
17.1 years ago Hervé Pagès 16k
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1.5k
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Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
GUI Cancer Breast hgu133plus2 PROcess rtracklayer microRNA GUI Cancer Breast hgu133plus2
17.1 years ago Steven McKinney ▴ 310
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1.7k
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Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
Cancer Breast rtracklayer microRNA Cancer Breast rtracklayer microRNA
updated 17.1 years ago by ★ 1.6k • written 17.1 years ago by ▴ 310
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4
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2.0k
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Creating a new instance of oligoSnpSet
Annotation Cancer Breast VanillaICE copynumber Annotation Cancer Breast VanillaICE
17.1 years ago Steven McKinney ▴ 310
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2
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801
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Download numbers
Cancer Cancer
updated 17.2 years ago by ▴ 760 • written 17.2 years ago by 16k
1,555 results • Page 18 of 32
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Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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