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0
replies
1.4k
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edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category
edgeR
Category
edgeR
14.2 years ago
Emanuel Heitlinger
▴ 30
0
votes
17
replies
3.2k
views
Coverage by base
Coverage
Coverage
14.3 years ago
rohan bareja
▴ 200
0
votes
0
replies
800
views
Sample Grouping
lumi
lumi
14.3 years ago
rajasereddy
▴ 10
0
votes
4
replies
1.5k
views
R/Bioconductor CDF to Affymetrix CDF
cdf
convert
cdf
convert
updated 14.3 years ago by
Benjamin Otto
▴ 10 • written 14.3 years ago by
Benjamin Otto
▴ 830
0
votes
4
replies
2.0k
views
edgeR design matrix
PROcess
edgeR
PROcess
edgeR
updated 14.3 years ago by
Gordon Smyth
53k • written 14.3 years ago by
lpascual
▴ 50
0
votes
1
reply
1.0k
views
question about affymetrix array:ht-hg-u133acdf
Microarray
cdf
Microarray
cdf
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.5k
views
Postdoctoral Position in Statistical Genomics - Zurich
ASSET
ASSET
14.3 years ago
Mark Robinson
▴ 880
0
votes
1
reply
1.6k
views
RNA-Seq : comparison cuffdiff, edgeR, Partek
edgeR
edgeR
updated 14.3 years ago by
vasu punj
▴ 80 • written 14.3 years ago by
Lana Schaffer
★ 1.3k
1
vote
1
reply
2.5k
views
Problem with a specific GEO dataset.
GEOquery
GEOquery
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
Regarding subread vignette
Sequencing
Alignment
Rsubread
Sequencing
Alignment
Rsubread
14.3 years ago
Wei Shi
★ 3.6k
1
vote
2
replies
2.1k
views
Limma model parameters design, combining a paired with a factorial design
limma
limma
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
john herbert
▴ 560
0
votes
3
replies
2.6k
views
postForm in RCurl
14.3 years ago
Voke AO
▴ 760
0
votes
1
reply
1.5k
views
EdgeR: Log FC does not changes when I swap the groups
edgeR
edgeR
updated 14.3 years ago by
Gordon Smyth
53k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
best annotation package for drosophila (agilent gene expression)?
Annotation
Agi4x44PreProcess
Annotation
Agi4x44PreProcess
14.3 years ago
Jarek Bryk
▴ 110
0
votes
2
replies
2.3k
views
Is it possible to generate an ExpressionSet object that contain duplicate row names?
Annotation
Annotation
updated 14.3 years ago by
Tim Triche
★ 4.2k • written 14.3 years ago by
nqueralt@clinic.ub.es
▴ 60
0
votes
0
replies
1.2k
views
a question about getCdfInfo package in GCRMA, thanks for your help.
Annotation
cdf
makecdfenv
Annotation
cdf
makecdfenv
14.3 years ago
boczniak767
▴ 740
0
votes
0
replies
864
views
BSgenome package for sacCer3
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
14.3 years ago
Hervé Pagès
16k
0
votes
0
replies
844
views
Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?
Pathways
Pathways
14.3 years ago
Peng Yu
▴ 950
0
votes
5
replies
1.7k
views
need help with SNP6.0 quantile normalization
SNP
Normalization
cdf
SNP
Normalization
cdf
updated 14.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.3 years ago by
qian liu
▴ 30
0
votes
0
replies
1.5k
views
[Job] Functional genomic analysis of cancer/RNAi screening
Transcription
Sequencing
Genetics
Pathways
Cancer
Prostate
Transcription
Sequencing
Cancer
14.3 years ago
Sean Davis
21k
0
votes
1
reply
1.9k
views
read.maimage error message
updated 14.3 years ago by
boczniak767
▴ 740 • written 14.3 years ago by
Guest User
★ 13k
0
votes
2
replies
2.6k
views
Installing packages on R v2.13.2, OSX multiple warning messages
Annotation
cdf
probe
affy
gcrma
Annotation
cdf
probe
affy
gcrma
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
962
views
ChIPpeakAnno - for genes with multiple isoforms
Transcription
Annotation
annotate
ChIPpeakAnno
Transcription
Annotation
annotate
14.3 years ago
Julie Zhu
★ 4.3k
0
votes
0
replies
1.1k
views
Fwd: Problems with edgeR for differential expression
Normalization
limma
edgeR
DESeq
Normalization
limma
edgeR
DESeq
14.3 years ago
Nick Schurch
▴ 60
0
votes
4
replies
1.8k
views
Problems with edgeR for differential expression
Normalization
edgeR
Normalization
edgeR
updated 14.3 years ago by
Nick Schurch
▴ 60 • written 14.3 years ago by
Gordon Smyth
53k
0
votes
1
reply
917
views
report a problem
updated 14.3 years ago by
Harris A. Jaffee
▴ 590 • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
1
reply
919
views
still the trimLRPatterns problem
updated 14.3 years ago by
Harris A. Jaffee
▴ 590 • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
0
replies
1.6k
views
Bioinformatics course - October 2011 Registration is now open
Microarray
Cancer
biomaRt
ArrayExpress
genomes
SANTA
Microarray
Cancer
biomaRt
genomes
14.3 years ago
Claude Chelala
▴ 40
0
votes
2
replies
1.8k
views
Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)
snpStats
snpStats
updated 14.3 years ago by
Martin Morgan
25k • written 14.3 years ago by
Tim Triche
★ 4.2k
0
votes
8
replies
4.4k
views
Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts
updated 14.3 years ago by
Wei Shi
★ 3.6k • written 14.3 years ago by
Tim Triche
★ 4.2k
0
votes
1
reply
1.9k
views
heat map for a time course study
updated 14.3 years ago by
Thomas Hampton
▴ 750 • written 14.3 years ago by
blockaa@huskers.unl.edu
▴ 30
0
votes
2
replies
1.9k
views
(BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem
Sus scrofa
BSgenome
BSgenome
Sus scrofa
BSgenome
BSgenome
updated 14.3 years ago by
Hervé Pagès
16k • written 14.3 years ago by
Elisabetta Manduchi
▴ 160
0
votes
1
reply
756
views
how to deal with Fastq file more than 30G
updated 14.3 years ago by
Steve Lianoglou
★ 13k • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
0
replies
1.2k
views
Mapping deletions onto chromosome ideograms
quantsmooth
quantsmooth
14.3 years ago
Srinivas Srikanth
▴ 70
0
votes
6
replies
1.8k
views
arrayQualityMetrics NULL XML-node Error; Anyone still getting this?
arrayQualityMetrics
arrayQualityMetrics
updated 14.3 years ago by
Wolfgang Huber
★ 13k • written 14.3 years ago by
Paniagua, Eric
▴ 30
0
votes
1
reply
725
views
Fwd: Creating One Single Object with Phenotype and Expression Data
GO
Cancer
GO
Cancer
updated 14.3 years ago by
Wolfgang Huber
★ 13k • written 14.3 years ago by
Ben Ganzfried
▴ 30
0
votes
2
replies
1.5k
views
Merge dataframes
14.3 years ago
João Daniel Nunes Duarte
▴ 30
0
votes
2
replies
1.6k
views
about refseq_dna in biomat
biomaRt
biomaRt
updated 14.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 14.3 years ago by
Ou, Jianhong
★ 1.3k
0
votes
0
replies
939
views
Merge dataframes
Genetics
Genetics
14.3 years ago
Aleš Maver
▴ 80
0
votes
0
replies
1.0k
views
Analysis of Affymetrix Cytogenetic Whole-Genome 2.7M array
Annotation
Annotation
14.3 years ago
Lavinia Gordon
▴ 480
0
votes
1
reply
1.9k
views
[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer
Biostrings
GLAD
Cancer
Biostrings
GLAD
updated 14.3 years ago by
Michael Lawrence
★ 11k • written 14.3 years ago by
Hervé Pagès
16k
0
votes
0
replies
1.2k
views
Pie chart
GO
GeneAnswers
GO
GeneAnswers
14.3 years ago
Guest User
★ 13k
0
votes
0
replies
1.0k
views
Bioconductor Digest, Vol 104, Issue 7
GO
AnnotationFuncs
GO
AnnotationFuncs
14.3 years ago
Stefan McKinnon Høj-Edwards
▴ 20
0
votes
0
replies
1.3k
views
GetEnrichedGo term
Yeast
biomaRt
Yeast
biomaRt
14.3 years ago
Julie Zhu
★ 4.3k
0
votes
5
replies
7.4k
views
how to update a bioconductor package
updated 14.3 years ago by
Hervé Pagès
16k • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
0
replies
916
views
Creating One Single Object with Phenotype and Expression Data
Cancer
Cancer
14.3 years ago
Ben Ganzfried
▴ 30
0
votes
0
replies
1.2k
views
Problems with edgeR for differential expression.
Normalization
edgeR
Normalization
edgeR
14.3 years ago
Nick Schurch
▴ 60
0
votes
4
replies
1.6k
views
Agi4x44PreProcess package: Error in build.est
Agi4x44PreProcess
Agi4x44PreProcess
updated 14.3 years ago by
Francois Pepin
▴ 80 • written 14.3 years ago by
Jon Mohl
▴ 20
0
votes
0
replies
1.2k
views
Conference announcement: Omics and Personalised Health, EMBL Heidelberg, 16-18 February 2012
genomes
genomes
14.3 years ago
Wolfgang Huber
★ 13k
0
votes
1
reply
1.5k
views
[question] integration of microarray data from different sources in limma package
Microarray
limma
BRAIN
Microarray
limma
BRAIN
updated 14.3 years ago by
Andreas Heider
▴ 340 • written 14.3 years ago by
이선재
▴ 30
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Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaas33ocissalpc
• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Votes
Answer: Where do the filename come from in the LOLA datasets?
Bioconductor Maintainer Application
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
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