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cancer
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0
votes
0
replies
938
views
A question about criteria for calling gain and loss in aCGH data
aCGH
Cancer
aCGH
aCGH
Cancer
aCGH
17.5 years ago
affy snp
▴ 640
0
votes
3
replies
1.2k
views
SPECIAL 20% OFF DISCOUNT ON A NEW BOOK FROM CRC PRESS
Cancer
Cancer
written 17.5 years ago by
Thomas, Judy
▴ 40
0
votes
4
replies
1.5k
views
LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)
Cancer
gcrma
Cancer
gcrma
updated 17.5 years ago by
Zhijin Wu
▴ 260 • written 17.5 years ago by
Richard Friedman
★ 2.0k
0
votes
9
replies
2.5k
views
gains and losses via mode shifting
Cancer
CGH
Cancer
CGH
17.6 years ago
Oscar Rueda
▴ 60
0
votes
0
replies
969
views
Pd info package affy 10K array
Microarray
Annotation
Network
Cancer
cdf
probe
affy
Microarray
Annotation
Network
Cancer
17.6 years ago
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
1.2k
views
kOverA(k, A=100, na.rm=TRUE)
GO
Preprocessing
Cancer
genefilter
limma
GO
Preprocessing
Cancer
genefilter
limma
updated 17.6 years ago by
rgentleman
★ 5.5k • written 17.6 years ago by
Roberts, Raymond
▴ 30
0
votes
0
replies
1.2k
views
cross study comparison of cell populations
Cancer
affy
metaArray
Cancer
affy
metaArray
17.6 years ago
Max Kauer
▴ 140
0
votes
0
replies
765
views
GCRMA-induced correlations? LARGE Change in GCRMA expression values (REPEAT QUESTION)
Microarray
Normalization
Cancer
gcrma
Microarray
Normalization
Cancer
gcrma
17.6 years ago
Richard Friedman
★ 2.0k
0
votes
1
reply
913
views
R 2.7.1
Cancer
Cancer
updated 17.6 years ago by
Sean Davis
21k • written 17.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
2
replies
1.5k
views
CGH-like workflow for Affymetrix SNP 500k
aCGH
SNP
Cancer
DNAcopy
aCGH
aCGH
SNP
Cancer
DNAcopy
aCGH
updated 17.6 years ago by
Henrik Bengtsson
★ 2.4k • written 17.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
656
views
Fwd: Re: html "help"
Microarray
Cancer
Microarray
Cancer
updated 17.6 years ago by
James W. MacDonald
68k • written 17.6 years ago by
Naomi Altman
★ 6.0k
1
vote
0
replies
1.9k
views
Agilent - importing and reading problems
Microarray
Cancer
limma
Microarray
Cancer
limma
17.6 years ago
Bernal-Mizrachi, Leon
▴ 50
0
votes
3
replies
1.1k
views
Find Affy probes within a particular region
Annotation
GO
Cancer
biomaRt
Annotation
GO
Cancer
biomaRt
updated 17.6 years ago by
James W. MacDonald
68k • written 17.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
1.0k
views
GSEA GeneSetCollection for GO info from Illumina annotation package
Annotation
GO
Cancer
Annotation
GO
Cancer
17.6 years ago
Martin Morgan
25k
0
votes
2
replies
1.5k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 17.6 years ago by
Paul Geeleher
★ 1.3k • written 17.6 years ago by
Gordon Smyth
53k
0
votes
0
replies
940
views
Possible Bug in readExpressionSet
Cancer
Biobase
Cancer
Biobase
17.6 years ago
Martin Morgan
25k
0
votes
0
replies
1.1k
views
Jobs
Cancer
Cancer
17.6 years ago
Crispin Miller
★ 1.1k
0
votes
2
replies
1.6k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 17.6 years ago by
rgentleman
★ 5.5k • written 17.6 years ago by
Paul Geeleher
★ 1.3k
0
votes
0
replies
787
views
Problem viewing vignettes : openPDF and pdfviewer and possible fix
Cancer
Biobase
Cancer
Biobase
17.6 years ago
Martin Morgan
25k
0
votes
0
replies
1.2k
views
missing probes from illuminaHumanv3ProbeID.db
Annotation
Cancer
bgx
Annotation
Cancer
bgx
17.6 years ago
Lynn Amon
▴ 280
0
votes
0
replies
1.2k
views
Rank Products- breast cancer
Cancer
RankProd
Cancer
RankProd
17.7 years ago
Eleni Christodoulou
▴ 150
0
votes
0
replies
1.9k
views
open Junior group leader position, Medical University of Innsbruck, Austria
Proteomics
Cancer
microRNA
tRanslatome
Proteomics
Cancer
microRNA
tRanslatome
17.7 years ago
Johannes Rainer
▴ 300
0
votes
0
replies
870
views
Employment opportunities
Network
Cancer
Network
Cancer
17.7 years ago
Martin Morgan
25k
0
votes
0
replies
656
views
BioC 2008 updates
Cancer
Cancer
17.7 years ago
rgentleman
★ 5.5k
0
votes
3
replies
1.8k
views
Specific annotation information from ExpressionSet
Annotation
Cancer
probe
Annotation
Cancer
probe
updated 17.7 years ago by
Martin Morgan
25k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
1.6k
views
Bioinformatics Faculty Position available at UCSF Cancer Center
Proteomics
Cancer
Proteomics
Cancer
17.7 years ago
Ru-Fang Yeh
▴ 20
0
votes
0
replies
1.5k
views
Variance correction, coxph or cph model
Cancer
Cancer
17.7 years ago
Aedin Culhane
▴ 510
0
votes
5
replies
3.7k
views
Finding genes with significant linear regression or trend
Microarray
Regression
Cancer
limma
DOSE
Microarray
Regression
Cancer
limma
DOSE
updated 17.7 years ago by
Ana Conesa
▴ 340 • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
1.3k
views
Rtreemix (NEW package)
Cancer
HIV
Rtreemix
Cancer
HIV
Rtreemix
17.7 years ago
Jasmina Bogojeska
▴ 30
0
votes
2
replies
1.8k
views
GSEABase how to map gene symbols to mouse EntrezId or Affy
Cancer
affy
Cancer
affy
17.7 years ago
Martin Morgan
25k
0
votes
1
reply
824
views
GCRMA-induced correlations? LARGE Change in GCRMA expression values
Microarray
Normalization
Cancer
gcrma
Microarray
Normalization
Cancer
gcrma
updated 17.7 years ago by
Guido Hooiveld
★ 4.1k • written 17.7 years ago by
Richard Friedman
★ 2.0k
0
votes
0
replies
614
views
Bioinformatics Engineer for Deep Sequencing
Cancer
Cancer
17.7 years ago
N S
▴ 10
0
votes
1
reply
966
views
Limma: Design matrix question
Microarray
Cancer
Microarray
Cancer
updated 17.7 years ago by
John Fernandes
▴ 100 • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
1.1k
views
snapCGH and Nimblegen arrays
Cancer
snapCGH
Cancer
snapCGH
17.7 years ago
Gareth Wilson
▴ 10
0
votes
3
replies
1.3k
views
aCGH package - performance Issues
SNP
Cancer
SNP
Cancer
17.7 years ago
Julian Lee
▴ 140
0
votes
3
replies
2.1k
views
ExpressionSet or MAList
Annotation
ExperimentData
Cancer
Annotation
ExperimentData
Cancer
updated 17.7 years ago by
Gordon Smyth
53k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
811
views
ExpressionSet or MAList
Microarray
Annotation
Cancer
Microarray
Annotation
Cancer
updated 17.7 years ago by
Wolfgang Huber
★ 13k • written 17.7 years ago by
Gordon Smyth
53k
0
votes
0
replies
2.2k
views
Bioinformatics Positions, National Cancer Centre Singapore
Microarray
Epigenetics
Cancer
Microarray
Epigenetics
Cancer
17.7 years ago
Julian Lee
▴ 140
0
votes
3
replies
1.2k
views
MIAME object and abstract
Cancer
Cancer
updated 17.7 years ago by
Martin Morgan
25k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.1k
views
Detection above background (dabg) within bioconductor
Cancer
Cancer
updated 17.7 years ago by
cstrato
★ 3.9k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.7k
views
BioC 2.2 now available
SNP
Microarray
Genetics
Annotation
Preprocessing
Bayesian
Clustering
Infrastructure
Cancer
updated 17.7 years ago by
Patrick Aboyoun
★ 1.6k • written 17.7 years ago by
Martin Morgan
25k
0
votes
0
replies
695
views
Cutoff for non-specific gene filtering?
Cancer
Cancer
17.7 years ago
Suraj Menon
▴ 50
0
votes
1
reply
1.1k
views
Separate function edit window in Linux
Cancer
Cancer
updated 17.7 years ago by
Ramon Diaz
★ 1.1k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
873
views
ExpressionSet or MAList
Microarray
Annotation
Cancer
Microarray
Annotation
Cancer
updated 17.7 years ago by
Martin Morgan
25k • written 17.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.7k
views
Bug report: Help pages for degree (package graph) not displayed
Cancer
graph
SNAData
Cancer
graph
SNAData
updated 17.7 years ago by
Patrick Aboyoun
★ 1.6k • written 17.7 years ago by
Martin Morgan
25k
0
votes
0
replies
1.6k
views
Bioinformatics Positions, M. D. Anderson Cancer Center
Proteomics
Cancer
Proteomics
Cancer
17.8 years ago
caiwei@mdanderson.org
▴ 110
0
votes
4
replies
1.5k
views
mouse4302.db vs mouse 4302
Annotation
Cancer
mouse4302
Annotation
Cancer
mouse4302
updated 17.8 years ago by
Marc Carlson
★ 7.2k • written 17.8 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
792
views
Limma: import files with genes missing
Annotation
Cancer
probe
limma
ASSIGN
Annotation
Cancer
probe
limma
ASSIGN
17.8 years ago
Gordon Smyth
53k
0
votes
0
replies
822
views
Limma: import files with genes missing
Cancer
probe
limma
Cancer
probe
limma
17.8 years ago
Daniel Brewer
★ 1.9k
0
votes
3
replies
1.4k
views
mouse4302,db_2.0.2 in AffylmGUI
Annotation
Cancer
mouse4302
affy
limma
Annotation
Cancer
mouse4302
affy
limma
updated 17.8 years ago by
Keith Satterley
▴ 450 • written 17.8 years ago by
Richard Friedman
★ 2.0k
1,555 results • Page
20 of 32
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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