1
vote
10
replies
6.3k
views
Rsubread package not available? Warning resolved
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updated 14.1 years ago by ★ 3.6k • written 14.1 years ago by ▴ 20
0
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0
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1.1k
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unimplemented options select=last and select=arbitrary in findOverlaps for GRanges
14.1 years ago Janet Young ▴ 740
0
votes
2
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1.7k
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cellHTS2 variance by plate calculation?
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updated 14.1 years ago by ▴ 160 • written 14.1 years ago by ★ 13k
0
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0
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1.3k
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Help on cghMCR units of gapAllowed
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14.1 years ago nac ▴ 280
0
votes
0
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1.0k
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how to analyze
affy microRNA affy microRNA
14.1 years ago Adrian Johnson ▴ 330
0
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1
reply
1.8k
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Summarising Probe Sets for Agilent 4x44 Arrays
Clustering probe PROcess Clustering probe PROcess
updated 14.1 years ago by ▴ 80 • written 14.1 years ago by ▴ 10
0
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0
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982
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preprocessing pipeline of aglient Custom GE 8x15k single color array
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14.1 years ago Justin ▴ 10
0
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0
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Job: Seeking a Postdoctoral Researcher or Research Associate , RIKEN Yokohama Institute, Japan
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14.1 years ago Dr. Sujatha Mohan ▴ 10
0
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2
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1.4k
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library size and fold changes
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updated 21 months ago by 53k • written 14.1 years ago by ▴ 670
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3
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how to install gnGNF1a cdf and probe files to a recent version of R (2.13.1)?
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updated 14.1 years ago by 68k • written 14.1 years ago by ▴ 30
0
votes
3
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3.9k
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Trying to use the liftOver function from the rtracklayer package in R 2.14.0
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updated 14.1 years ago by ★ 11k • written 14.1 years ago by ★ 1.1k
0
votes
1
reply
1.4k
views
countOverlaps, package:IRanges (Michael Lawrence)
updated 14.1 years ago by ★ 11k • written 14.1 years ago by ▴ 10
0
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2
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1.7k
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simple limma question (read.ilmn)
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14.1 years ago Kripa R ▴ 180
0
votes
0
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SPIA package
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14.1 years ago Tarca, Adi ▴ 570
1
vote
1
reply
1.5k
views
how to match a regular expression to XString, XStringViews or MaskedXString object
updated 14.1 years ago by ▴ 590 • written 14.1 years ago by ★ 2.0k
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2
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1.7k
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arrayQualityMetrics subscript out of bounds error and Harshlight error
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updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 180
0
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0
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738
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Median/Quantile values table
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14.1 years ago Guest User ★ 13k
0
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1
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1.0k
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using GenomicFeature
SNP SNP
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 70
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0
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Inconsistency in illuminaHumanv4.db ?
Annotation Annotation
14.1 years ago Mark Dunning ★ 1.1k
0
votes
0
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1.3k
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Job: Biostatistician/Bioinformatician, University of Cambridge, UK
Genetics Arabidopsis thaliana PROcess Genetics Arabidopsis thaliana PROcess
14.1 years ago Krys Kelly ▴ 270
0
votes
1
reply
790
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Error with package ExpressionView
GO GO
updated 14.1 years ago by ★ 6.8k • written 14.1 years ago by ★ 13k
0
votes
2
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1.0k
views
error in DEXSeq fitDispersionFunction()
DEXSeq DEXSeq
updated 14.1 years ago by ▴ 120 • written 14.1 years ago by ★ 13k
0
votes
0
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1.5k
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GenomeGraphs plots: polygon tracks for sequencing coverage data
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14.1 years ago Samuel Wuest ▴ 330
0
votes
6
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3.0k
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Error when using the nsFilter command in the genefilter package
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14.1 years ago Peter Davidsen ▴ 210
0
votes
1
reply
773
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NucleR: processReads/solveUserSEW0 - Error
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updated 14.1 years ago by ▴ 50 • written 14.1 years ago by ▴ 70
0
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0
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question for SPIA package
Pathways SPIA Pathways SPIA
14.1 years ago Jing Huang ▴ 380
0
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0
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1.6k
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[Job] Bioinformatician-NGS (Vienna, Austria)
Sequencing Infrastructure Sequencing Infrastructure
14.1 years ago Ido M. Tamir ▴ 150
0
votes
2
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1.5k
views
DEXSeq availability
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updated 14.1 years ago by ★ 8.2k • written 14.1 years ago by ★ 13k
0
votes
0
replies
1.4k
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lumiR Does Not Create lumi Batch
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14.1 years ago Sean Davis 21k
0
votes
3
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1.7k
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DESeq variance question
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updated 14.1 years ago by 53k • written 14.1 years ago by ▴ 10
0
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1
reply
1.3k
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lumiR Does Not Create lumi Batch
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updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 750
0
votes
3
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arrayQualityMetrics produces non-interactive PCA plot (Figure 3)
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14.1 years ago Vladimir Zhurov ▴ 70
0
votes
1
reply
1.2k
views
intragenic sequence extraction
Annotation Cancer Organism BSgenome BSgenome GenomicFeatures Annotation Cancer Organism
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 90
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votes
2
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1.5k
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Limma Dual Color Agilent : Mixed model or not?
limma limma
14.1 years ago Gordon Smyth 53k
0
votes
0
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3.0k
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Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
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14.1 years ago Gordon Smyth 53k
0
votes
1
reply
1.4k
views
arrayQualityMetrics: expression or probe-level data?
Cancer gcrma Cancer gcrma
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 20
0
votes
0
replies
882
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comparison between two toptable
14.1 years ago Alberto Goldoni ▴ 420
0
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2
replies
1.3k
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some basic questions
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updated 14.1 years ago by ★ 2.0k • written 14.1 years ago by ▴ 40
0
votes
2
replies
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Restoring TranscriptDb object crashes R-session
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 50
0
votes
5
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2.2k
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cummeRbund Error in Volcano Plot
14.1 years ago Chintan Vora - Xcelris ▴ 70
0
votes
0
replies
1.3k
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using GAIA
gaia gaia
14.1 years ago viritha kaza ▴ 580
0
votes
1
reply
1.4k
views
custom SNPlocs / BSgenome package
SNP Annotation Organism Homo sapiens BSgenome SNPlocs BSgenome SNP Annotation Organism
updated 14.1 years ago by 16k • written 14.1 years ago by ▴ 100
0
votes
0
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edgeR - R script - results compared to DESeq
GLAD edgeR DESeq GLAD edgeR DESeq
14.1 years ago Gordon Smyth 53k
0
votes
0
replies
739
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edgeR on microRNA data
14.1 years ago David Fredman ▴ 10
0
votes
5
replies
1.5k
views
biocLite, ask=FALSE bug
updated 14.1 years ago by ★ 8.2k • written 14.1 years ago by ★ 6.5k
0
votes
3
replies
2.6k
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ddCt isn't working with exported ABI7500-RT-PACR file
convert ddCt convert ddCt
updated 14.1 years ago by ▴ 300 • written 14.1 years ago by ▴ 20
0
votes
0
replies
1.1k
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Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
GO GO
14.1 years ago Joern Toedling ▴ 50
0
votes
1
reply
792
views
Probe level normalization
Normalization probe affy limma Normalization probe affy limma
updated 14.1 years ago by 68k • written 14.1 years ago by ▴ 40
0
votes
2
replies
1.1k
views
issue with limma?
limma lumi limma lumi
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 180
1
vote
0
replies
1.8k
views
Bioconductor Employment: Statistical Research Associate
DNASeq Cancer DNASeq Cancer
14.1 years ago Martin Morgan 25k
46,723 results • Page 609 of 935
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
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
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
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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