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survival
•
reset
0
votes
10
replies
2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray
Annotation
GO
Network
Regression
Survival
Infrastructure
Escherichia coli
ROC
11.1 years ago
Julie Zhu
★ 4.3k
0
votes
8
replies
1.6k
views
oligo on R 2.4.1?
GO
Survival
annotate
genefilter
affy
affydata
matchprobes
affyQCReport
affyio
oligo
GO
updated 17.2 years ago by
Seth Falcon
★ 7.4k • written 17.2 years ago by
Jenny Drnevich
★ 2.2k
0
votes
8
replies
2.0k
views
AnnBuilder and Kegg
Pathways
GO
Survival
Cancer
Organism
annotate
affydata
vsn
AnnBuilder
globaltest
GO
vsn
updated 17.5 years ago by
David Lapointe
▴ 190 • written 17.5 years ago by
John Zhang
★ 2.9k
0
votes
10
replies
1.9k
views
Some Genefilter questions
Normalization
Survival
Cancer
cdf
genefilter
geneplotter
affy
affydata
widgetTools
gcrma
updated 17.4 years ago by
Amy Mikhail
▴ 460 • written 17.4 years ago by
David K Pritchard
▴ 70
0
votes
6
replies
1.4k
views
Many missing GO terms from GOHyperG call using mgu74av2
GO
Survival
hgu95av2
mgu74av2
Ruuid
annotate
multtest
affy
graph
annaffy
RBGL
GOstats
updated 18.9 years ago by
Seth Falcon
★ 7.4k • written 18.9 years ago by
Dick Beyer
★ 1.4k
0
votes
5
replies
1.6k
views
Importing CDF file for custom array using makecdfenv
Microarray
GO
Survival
Cancer
cdf
Biobase
annotate
genefilter
affy
graph
makecdfenv
GO
updated 17.5 years ago by
Sung-Chur Sim
▴ 20 • written 17.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
7
replies
1.7k
views
problem with GOstats, developmental version?
GO
Survival
hgu95av2
annotate
affy
affydata
graph
Rgraphviz
limma
gcrma
matchprobes
GO
updated 16.7 years ago by
Seth Falcon
★ 7.4k • written 16.7 years ago by
Jenny Drnevich
★ 2.2k
0
votes
4
replies
1.2k
views
problems with Affy vignette and affybatch objects
GO
Survival
cdf
Biobase
annotate
genefilter
multtest
reposTools
affy
affydata
graph
GO
updated 17.5 years ago by
Martin Morgan
25k • written 17.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
11
replies
2.7k
views
trouble hacking plotPCA
GO
Survival
Biobase
genefilter
affy
affydata
graph
limma
gcrma
matchprobes
affyPLM
RBGL
updated 17.4 years ago by
Rustici, Gabriella NIH/NCI [F]
▴ 10 • written 17.4 years ago by
Jenny Drnevich
★ 2.2k
0
votes
3
replies
2.1k
views
gene expression data followup
Survival
Cancer
Survival
Cancer
updated 15.5 years ago by
James W. MacDonald
65k • written 15.5 years ago by
Adrian Johnson
▴ 330
0
votes
9
replies
1.8k
views
problem with duplicateCorrelation and ExpressionSet objects
GO
Survival
cdf
Biobase
graph
limma
gcrma
annaffy
affyPLM
simpleaffy
biomaRt
Category
updated 17.0 years ago by
Seth Falcon
★ 7.4k • written 17.0 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.1k
views
justRMA using incorrect default cdf
GO
Survival
rat2302
cdf
annotate
genefilter
affy
limma
affycoretools
GO
Survival
cdf
18.3 years ago • updated 18.2 years ago
Kimpel, Mark W
▴ 890
0
votes
3
replies
1.4k
views
error in mas5calls() for soybean chip
Survival
hu6800
cdf
probe
Biobase
genefilter
reposTools
affy
affydata
limma
gcrma
made4
updated 18.1 years ago by
Ken Simpson
▴ 70 • written 18.1 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.2k
views
applying coxfilter after LIMMA
Survival
Cancer
limma
Survival
Cancer
limma
updated 15.5 years ago by
James W. MacDonald
65k • written 15.5 years ago by
Adrian Johnson
▴ 330
0
votes
6
replies
3.4k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation
GO
Survival
ExperimentData
cdf
DynDoc
genefilter
geneplotter
multtest
affy
GO
updated 16.7 years ago by
Weiyin Zhou
▴ 220 • written 16.7 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.6k
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO
Survival
Biobase
genefilter
affy
limma
RBGL
GOstats
Category
affyio
affycoretools
GO
17.2 years ago
Mark W Kimpel
▴ 830
0
votes
2
replies
1.0k
views
2fold sigchanges from limma
GO
Survival
hgu133a2
annotate
hexbin
limma
gcrma
matchprobes
annaffy
GO
Survival
hexbin
updated 17.4 years ago by
Gordon Smyth
50k • written 17.4 years ago by
Ivan Baxter
▴ 60
0
votes
2
replies
1.2k
views
simpleaffy and yeast2cdf problems
Survival
cdf
genefilter
affy
simpleaffy
Survival
cdf
genefilter
affy
simpleaffy
updated 17.3 years ago by
Alvord, Greg DMS [Contr]
▴ 160 • written 17.3 years ago by
Dan Swan
▴ 50
0
votes
12
replies
1.9k
views
Some Genefilter questions
GO
Survival
cdf
genefilter
geneplotter
tkWidgets
affy
affydata
widgetTools
gcrma
affyPLM
updated 17.4 years ago by
rgentleman
★ 5.5k • written 17.4 years ago by
Amy Mikhail
▴ 460
0
votes
3
replies
838
views
multtest dependencies
Survival
genefilter
multtest
reposTools
Survival
genefilter
multtest
reposTools
19.1 years ago
Francois Pepin
★ 1.3k
0
votes
8
replies
3.2k
views
Reading Agilent files using read.maimages
Survival
DynDoc
genefilter
tkWidgets
affy
vsn
marray
convert
ArrayExpress
Survival
affy
updated 16.7 years ago by
Scott Reagan Franklin
▴ 20 • written 16.7 years ago by
Steve Taylor
▴ 100
0
votes
2
replies
4.6k
views
Problem installing \'survival\' package/ Fix request + other options?
Survival
Survival
updated 10.8 years ago by
James W. MacDonald
65k • written 10.8 years ago by
Guest User
★ 13k
0
votes
2
replies
778
views
A question on GO annotations
Survival
Survival
updated 17.6 years ago by
Oosting, J. PATH
▴ 550 • written 17.6 years ago by
Narinder Singh Sahni
▴ 50
0
votes
2
replies
1.6k
views
"AveExp" column has dissappeared from limma topTable
GO
Survival
annotate
geneplotter
affydata
limma
annaffy
affyPLM
GO
Survival
annotate
updated 17.1 years ago by
Gordon Smyth
50k • written 17.1 years ago by
Marcus Davy
▴ 680
0
votes
2
replies
1.4k
views
'Factorial Design' package question
Survival
cdf
multtest
affy
factDesign
biomaRt
Survival
cdf
multtest
affy
factDesign
15.9 years ago
Glazko, Galina
▴ 350
0
votes
2
replies
1.5k
views
problem loading affycoretools
Survival
hgu95av2
Biobase
Ruuid
annotate
genefilter
multtest
affydata
graph
limma
gcrma
17.7 years ago
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.1k
views
vsm2
Survival
geneplotter
affy
vsn
limma
affyio
Survival
geneplotter
affy
vsn
limma
affyio
updated 16.6 years ago by
Wolfgang Huber
★ 13k • written 16.6 years ago by
Richard Harrison
▴ 70
0
votes
2
replies
838
views
subset eset by row broken
Survival
rgu34a
multtest
affy
Survival
rgu34a
multtest
affy
18.0 years ago
Kimpel, Mark W
▴ 890
0
votes
2
replies
1.2k
views
Chromosome 23 and 24 dropped after run snapCGH processCGH
aCGH
Survival
Cancer
annotate
genefilter
affy
DNAcopy
aCGH
GLAD
tilingArray
snapCGH
updated 16.6 years ago by
J-C. Marioni
▴ 40 • written 16.6 years ago by
caiwei@mdanderson.org
▴ 110
0
votes
3
replies
1.9k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP
Sequencing
miRNA
Microarray
Annotation
Normalization
Pathways
Preprocessing
Survival
updated 13.1 years ago by
Ivan Gregoretti
▴ 310 • written 13.1 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
1
reply
1.1k
views
Newbie 'rflowcyt' question; problem loading facscan256.fcs
Survival
Infrastructure
Cancer
hexbin
prada
rfcdmin
rflowcyt
Survival
Infrastructure
updated 17.9 years ago by
Seth Falcon
★ 7.4k • written 17.9 years ago by
Ulrik Stervbo
▴ 80
0
votes
1
reply
920
views
New package
Survival
Survival
19.9 years ago
Jeff Gentry
★ 3.9k
0
votes
1
reply
725
views
just.gcrma and gcrma
Survival
Cancer
Lung
Survival
Cancer
Lung
updated 20.0 years ago by
James W. MacDonald
65k • written 20.0 years ago by
Oosting, J. PATH
▴ 550
0
votes
4
replies
1.3k
views
problems rma() with mouse exon affy data in exonmap package
Survival
cdf
genefilter
affy
simpleaffy
plier
exonmap
Survival
cdf
genefilter
affy
updated 16.7 years ago by
James W. MacDonald
65k • written 16.7 years ago by
bruce
▴ 20
0
votes
1
reply
4.2k
views
R package Installation Errors
Survival
Biobase
affy
Survival
Biobase
affy
updated 18.3 years ago by
Martin Morgan
25k • written 18.3 years ago by
Zhang, Jacob Zhongfa
▴ 60
0
votes
1
reply
1.3k
views
Job Posting in Biostatistics/Statistics
Bayesian
Survival
Cancer
PROcess
ASSET
Bayesian
Survival
Cancer
PROcess
ASSET
updated 21.4 years ago by
Johannes Hüsing
▴ 80 • written 21.4 years ago by
Janusz Kawczak
▴ 10
0
votes
1
reply
964
views
Normalization in davidTiling demo
Normalization
GO
Survival
genefilter
geneplotter
affy
vsn
tilingArray
affyio
GO
Survival
updated 17.2 years ago by
Wolfgang Huber
★ 13k • written 17.2 years ago by
Julian Gehring
★ 1.3k
0
votes
1
reply
2.8k
views
Displaying multiple survival curves on one graph
Survival
graph
Survival
graph
updated 18.4 years ago by
Seth Falcon
★ 7.4k • written 18.4 years ago by
Rifat Hamoudi
▴ 30
0
votes
1
reply
1.1k
views
Exonmap mapping problems
Survival
genefilter
affy
plier
affyio
exonmap
Survival
genefilter
affy
plier
affyio
updated 16.7 years ago by
Michal Okoniewski
▴ 120 • written 16.7 years ago by
Tore Eriksson
▴ 10
0
votes
1
reply
1.8k
views
using simpleaffy incorrectly, or is there a problem with the read.affy function?
Microarray
Survival
Cancer
genefilter
affy
simpleaffy
affyio
Microarray
Survival
Cancer
17.3 years ago
k. brand
▴ 420
0
votes
1
reply
1.5k
views
simpleaffy segmentation fault
Survival
probe
genefilter
affy
affyio
Survival
probe
genefilter
affy
affyio
updated 9.0 years ago by
vlagani
• 0 • written 17.3 years ago by
Sucheta Tripathy
▴ 170
0
votes
1
reply
3.2k
views
RE : create an new AnnotatedDataFrame
Annotation
Survival
Yeast
Biobase
genefilter
tkWidgets
marray
convert
arrayMagic
affyio
updated 16.7 years ago by
Martin Morgan
25k • written 16.7 years ago by
Yad Ghavi-Helm
▴ 30
0
votes
1
reply
3.3k
views
undefined columns selected error when using bagging{ipred}
Survival
Survival
updated 11.7 years ago by
Valerie Obenchain
★ 6.8k • written 11.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.6k
views
create an new AnnotatedDataFrame
Survival
Yeast
Biobase
genefilter
tkWidgets
marray
convert
arrayMagic
affyio
Survival
updated 16.8 years ago by
Martin Morgan
25k • written 16.7 years ago by
Yad Ghavi-Helm
▴ 30
0
votes
1
reply
1.2k
views
warning from make.cdf.package - FYI
GO
Survival
cdf
Biobase
annotate
genefilter
graph
makecdfenv
limma
gcrma
matchprobes
GO
updated 17.5 years ago by
James W. MacDonald
65k • written 17.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
1.2k
views
annaffy errors
GO
Survival
mgu74av2
cdf
annotate
affy
limma
gcrma
matchprobes
annaffy
simpleaffy
plier
updated 17.3 years ago by
James W. MacDonald
65k • written 17.3 years ago by
Ido M. Tamir
▴ 320
0
votes
1
reply
732
views
RMA warning message about missing se.exprs
Survival
Cancer
cdf
genefilter
simpleaffy
Survival
Cancer
cdf
genefilter
simpleaffy
updated 17.0 years ago by
Martin Morgan
25k • written 17.0 years ago by
caiwei@mdanderson.org
▴ 110
0
votes
3
replies
1.8k
views
Can't get RCurl...
GO
Survival
annotate
genefilter
affy
graph
limma
GOstats
biomaRt
Category
affycoretools
updated 17.1 years ago by
James W. MacDonald
65k • written 17.1 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
940
views
simpleaffy plot error
Survival
cdf
genefilter
simpleaffy
Survival
cdf
genefilter
simpleaffy
updated 17.0 years ago by
Crispin Miller
★ 1.1k • written 17.0 years ago by
Georg Otto
▴ 510
0
votes
3
replies
2.0k
views
Situation of the legend in the plotPCA of the affycoretools library
GO
Survival
cdf
annotate
genefilter
multtest
affy
graph
limma
RBGL
GOstats
Category
GO
updated 17.6 years ago by
James W. MacDonald
65k • written 17.6 years ago by
Jordi Altirriba Gutiérrez
▴ 350
50 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
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Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
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It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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