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Aurelio
18.0 years ago
Aurelio Irvin
▴ 10
0
votes
1
reply
468
views
test set validation in pdmclass package
updated 18.0 years ago by
James W. MacDonald
68k • written 18.0 years ago by
JONG-MIN LEE
▴ 50
0
votes
1
reply
771
views
Questions in GOvis.pdf - a GOStats vignette
GOstats
GOstats
updated 18.0 years ago by
Martin Morgan
25k • written 18.0 years ago by
Srinivas Iyyer
▴ 600
0
votes
0
replies
954
views
Nachricht uber eine radioaktive Kontamination in der Schweiz
18.0 years ago
Lawrence Madden
▴ 10
0
votes
2
replies
1.1k
views
agilent bicolor
updated 18.0 years ago by
Naomi Altman
★ 6.0k • written 18.0 years ago by
Marie-Paule Roth
▴ 40
0
votes
0
replies
1.1k
views
To many differentially expressed genes produced by LIMMA and dye-effect question
Microarray
Normalization
limma
Microarray
Normalization
limma
18.0 years ago
krasikov@science.uva.nl
▴ 100
0
votes
0
replies
1.5k
views
Inf values using SAM (package=siggenes)
Annotation
Survival
Cancer
genefilter
affy
limma
maDB
affyio
Annotation
Survival
Cancer
18.0 years ago
Holger Schwender
▴ 900
0
votes
1
reply
1.2k
views
GOStats - HyperGTest - expert opinion needed about the approach selecting gene list
updated 18.0 years ago by
James W. MacDonald
68k • written 18.0 years ago by
Srinivas Iyyer
▴ 600
0
votes
5
replies
2.1k
views
understanding GOstats p-value
Annotation
GO
Cancer
CGH
GOstats
Annotation
GO
Cancer
CGH
GOstats
updated 18.0 years ago by
Charles Berry
▴ 290 • written 18.0 years ago by
Janet Young
▴ 740
0
votes
0
replies
714
views
Limma: Trying to read in imagene files
limma
limma
18.0 years ago
Gordon Smyth
53k
0
votes
0
replies
815
views
Microsoft Office 2007 Enterprise for 79, Retails @ 899 (You Save 819)
18.0 years ago
Kevin Long
▴ 10
0
votes
1
reply
1.4k
views
Low-level analysis of custom microarrays
Microarray
Normalization
Cancer
probe
affy
limma
affyio
Microarray
Normalization
Cancer
updated 18.0 years ago by
Wolfgang Huber
★ 13k • written 18.0 years ago by
Martin Morgan
25k
0
votes
0
replies
960
views
Adobe Photoshop CS3 Extended MAC/XP/Vista for 89, Retails @ 999 (You Save 909)
18.0 years ago
Eli Griffin
▴ 10
0
votes
4
replies
1.7k
views
GOstats package - Graphical representation of enriched terms - Help needed
GO
GO
updated 18.0 years ago by
Sean Davis
21k • written 18.0 years ago by
Srinivas Iyyer
▴ 600
0
votes
0
replies
1.2k
views
Low-level analysis of custom microarrays
Microarray
probe
affy
affyio
Microarray
probe
affy
affyio
18.0 years ago
Teresa Colombo
▴ 10
0
votes
0
replies
841
views
error with biomaRt in mysql mode
Cancer
biomaRt
Cancer
biomaRt
18.0 years ago
Janet Young
▴ 740
0
votes
0
replies
874
views
Cluster stability estimation
clusterStab
clusterStab
18.0 years ago
Francois Pepin
★ 1.3k
0
votes
3
replies
1.4k
views
Odd isolated problem with GOstats
GO
limma
GOstats
GO
limma
GOstats
updated 18.0 years ago by
Marc Carlson
★ 7.2k • written 18.0 years ago by
Mark W Kimpel
▴ 830
0
votes
1
reply
826
views
Reading the Affymetrix data as .txt data (from GEO)
updated 18.0 years ago by
Sean Davis
21k • written 18.0 years ago by
Alex Tsoi
▴ 260
0
votes
4
replies
1.3k
views
Help needed with configuration function from cellHTS2 package
cellHTS
cellHTS
18.0 years ago
Shripad Sinari
▴ 50
0
votes
0
replies
498
views
Limma: Trying to read in imagene files
18.0 years ago
Sally
▴ 250
0
votes
4
replies
897
views
Illumina data problem
updated 18.0 years ago by
Sean Davis
21k • written 18.0 years ago by
affy snp
▴ 640
0
votes
0
replies
2.1k
views
limma: decideTests
limma
probe
affy
18.0 years ago • updated 3.0 years ago
Gordon Smyth
53k
0
votes
0
replies
785
views
EBImage Problem
Cancer
EBImage
Cancer
EBImage
18.0 years ago
Ellul Jason
▴ 20
0
votes
2
replies
962
views
EBImage Problem
updated 18.1 years ago by
Oleg Sklyar
▴ 260 • written 18.1 years ago by
Ellul Jason
▴ 20
0
votes
4
replies
877
views
affy Package install
updated 18.1 years ago by
Hervé Pagès
16k • written 18.1 years ago by
Vallejo, Roger
▴ 40
0
votes
0
replies
682
views
affy Package
oligo
oligo
18.1 years ago
Naomi Altman
★ 6.0k
0
votes
0
replies
1.4k
views
Inf values using SAM (package=siggenes)
Survival
Cancer
affy
limma
maDB
affyio
Survival
Cancer
affy
limma
maDB
affyio
18.1 years ago
Julian Lee
▴ 140
0
votes
4
replies
2.2k
views
How to map KEGG gene IDs to gene names?
Rattus norvegicus
Rattus norvegicus
updated 18.1 years ago by
Martin Morgan
25k • written 18.1 years ago by
Elliot Kleiman
▴ 150
0
votes
0
replies
1.1k
views
another quick question about Illumina annotation
Annotation
AnnBuilder
lumi
Annotation
AnnBuilder
lumi
18.1 years ago
Pan Du
★ 1.2k
0
votes
6
replies
1.0k
views
How to retrieve gene information
updated 18.1 years ago by
Martin Morgan
25k • written 18.1 years ago by
affy snp
▴ 640
0
votes
3
replies
954
views
Affy Package
updated 18.1 years ago by
Uwe Ligges
▴ 20 • written 18.1 years ago by
Vallejo, Roger
▴ 40
0
votes
1
reply
544
views
Possible to compare/normalize across different chip versions?
updated 18.1 years ago by
Kishor Tappita
▴ 340 • written 18.1 years ago by
Sam Volchenboum
▴ 20
0
votes
0
replies
626
views
nlme package
18.1 years ago
Vallejo, Roger
▴ 40
0
votes
6
replies
1.4k
views
RBGL function highlyConnSG not recognized
18.1 years ago
burak kutlu
▴ 200
0
votes
0
replies
409
views
chip on chip Ringo
18.1 years ago
Jinyan Huang
▴ 10
0
votes
0
replies
400
views
asking help for lumi package (annotation)
18.1 years ago
Pan Du
★ 1.2k
0
votes
1
reply
887
views
error with biomaRt in mysql mode
Cancer
biomaRt
Cancer
biomaRt
updated 18.1 years ago by
James W. MacDonald
68k • written 18.1 years ago by
Janet Young
▴ 740
0
votes
5
replies
1.2k
views
Affy normalization question
updated 18.1 years ago by
James W. MacDonald
68k • written 18.1 years ago by
Mark W Kimpel
▴ 830
0
votes
0
replies
317
views
To my highway
18.1 years ago
rendering go
▴ 10
0
votes
0
replies
683
views
questions on lumi
graph
lumi
graph
lumi
18.1 years ago
Pan Du
★ 1.2k
0
votes
0
replies
560
views
Cluster stability estimation
18.1 years ago
qinghua xu
▴ 110
0
votes
0
replies
555
views
on rocks
18.1 years ago
verbal of
▴ 10
0
votes
1
reply
768
views
I would like to join the BioConductor mailing list
updated 18.1 years ago by
Richard Pearson
▴ 390 • written 18.1 years ago by
Sameet Mehta
▴ 30
0
votes
1
reply
484
views
asking help for lumi package
updated 18.1 years ago by
Pan Du
★ 1.2k • written 18.1 years ago by
fabio manzo
▴ 10
0
votes
0
replies
561
views
Microarray Data Analyst - Open Position
18.1 years ago
Yasmina.Bauer@Actelion.Com
▴ 20
0
votes
0
replies
520
views
custom subset method / handling columns selection as logic in '...' parameter
18.1 years ago
Eric Lecoutre
▴ 40
0
votes
4
replies
1.5k
views
Biobase ExpressionSet: metadata on assayData
updated 18.1 years ago by
Martin Morgan
25k • written 18.1 years ago by
Eric Lecoutre
▴ 40
0
votes
0
replies
1.1k
views
custom subset method / handling columns selection as logic in '...' parameter
Cancer
Biobase
Cancer
Biobase
18.1 years ago
Martin Morgan
25k
0
votes
0
replies
373
views
To golden
18.1 years ago
breeding as
▴ 10
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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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