Showing : survival • reset
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1.9k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 460
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11
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2.7k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.4 years ago by ▴ 10 • written 17.4 years ago by ★ 2.2k
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10
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1.9k
views
Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 17.4 years ago by ▴ 460 • written 17.4 years ago by ▴ 70
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10
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2.4k
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assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
11.1 years ago Julie Zhu ★ 4.3k
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9
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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 ★ 7.4k • written 17.0 years ago by ★ 2.2k
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8
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1.6k
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oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 17.2 years ago by ★ 7.4k • written 17.2 years ago by ★ 2.2k
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8
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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 ▴ 20 • written 16.7 years ago by ▴ 100
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8
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2.0k
views
AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 17.5 years ago by ▴ 190 • written 17.5 years ago by ★ 2.9k
4
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7
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4.1k
views
DESeq2 for survival analysis
deseq2 survival rlog transformation
6.4 years ago array chip ▴ 420
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7
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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 ★ 7.4k • written 16.7 years ago by ★ 2.2k
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6
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5.2k
views
Issues installing DESeq2, installation path not writable, package: survival
deseq2 survival
updated 17 months ago by • 0 • written 3.8 years ago by • 0
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6
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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 ▴ 220 • written 16.7 years ago by ★ 2.2k
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6
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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 ★ 7.4k • written 18.9 years ago by ★ 1.4k
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5
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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 ▴ 20 • written 17.5 years ago by ★ 2.2k
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4
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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 65k • written 16.7 years ago by ▴ 20
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4
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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 25k • written 17.5 years ago by ★ 2.2k
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4
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1.4k
views
running time of snapCGH processCGH and runDNAcopy
aCGH Survival CGH annotate genefilter affy DNAcopy aCGH GLAD tilingArray snapCGH aCGH
updated 16.6 years ago by ▴ 230 • written 16.6 years ago by ▴ 110
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4
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297
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I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 11 weeks ago by ▴ 730 • written 11 weeks ago by • 0
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3
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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 ▴ 70 • written 18.1 years ago by ★ 2.2k
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3
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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 ▴ 310 • written 13.1 years ago by ★ 8.2k
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3
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838
views
multtest dependencies
Survival genefilter multtest reposTools Survival genefilter multtest reposTools
19.1 years ago Francois Pepin ★ 1.3k
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3
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1.6k
views
Bioconductor 2.3 is released
aCGH Sequencing miRNA Microarray Visualization Bayesian Classification Survival Yeast LPE
15.5 years ago Patrick Aboyoun ★ 1.6k
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3
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1.8k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
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3
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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 65k • written 17.6 years ago by ▴ 350
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3
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2.1k
views
gene expression data followup
Survival Cancer Survival Cancer
updated 15.5 years ago by 65k • written 15.5 years ago by ▴ 330
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2
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838
views
subset eset by row broken
Survival rgu34a multtest affy Survival rgu34a multtest affy
18.0 years ago Kimpel, Mark W ▴ 890
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2
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1.1k
views
justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
18.3 years ago Kimpel, Mark W ▴ 890
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2
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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
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2
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4.6k
views
Problem installing \'survival\' package/ Fix request + other options?
Survival Survival
updated 10.8 years ago by 65k • written 10.8 years ago by ★ 13k
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2
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1.8k
views
Kaplan Meier curve
Survival Survival
updated 11.9 years ago by ★ 2.0k • written 11.9 years ago by ▴ 200
0
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2
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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 50k • written 17.4 years ago by ▴ 60
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2
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1.2k
views
simpleaffy and yeast2cdf problems
Survival cdf genefilter affy simpleaffy Survival cdf genefilter affy simpleaffy
updated 17.3 years ago by ▴ 160 • written 17.3 years ago by ▴ 50
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2
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1.2k
views
affycoretools vennSelect problem
GO Survival annotate genefilter affy graph gcrma annaffy RBGL GOstats biomaRt affyio
updated 15.9 years ago by 65k • written 15.9 years ago by ▴ 30
0
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2
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778
views
A question on GO annotations
Survival Survival
updated 17.6 years ago by ▴ 550 • written 17.6 years ago by ▴ 50
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2
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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 50k • written 17.1 years ago by ▴ 680
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2
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1.2k
views
applying coxfilter after LIMMA
Survival Cancer limma Survival Cancer limma
updated 15.5 years ago by 65k • written 15.5 years ago by ▴ 330
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2
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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 ▴ 40 • written 16.6 years ago by ▴ 110
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2
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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
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2
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1.3k
views
problem with probes2tableBM
Annotation GO Survival hgu133a2 annotate genefilter affy graph gcrma matchprobes GOstats
updated 16.6 years ago by ▴ 500 • written 16.6 years ago by ▴ 510
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2
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1.1k
views
vsm2
Survival geneplotter affy vsn limma affyio Survival geneplotter affy vsn limma affyio
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 70
0
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2
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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
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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 ★ 7.4k • written 17.9 years ago by ▴ 80
0
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1
reply
920
views
New package
Survival Survival
19.9 years ago Jeff Gentry ★ 3.9k
0
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1
reply
725
views
just.gcrma and gcrma
Survival Cancer Lung Survival Cancer Lung
updated 20.0 years ago by 65k • written 20.0 years ago by ▴ 550
0
votes
1
reply
4.2k
views
R package Installation Errors
Survival Biobase affy Survival Biobase affy
updated 18.3 years ago by 25k • written 18.3 years ago by ▴ 60
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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 ▴ 80 • written 21.4 years ago by ▴ 10
0
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1
reply
965
views
Normalization in davidTiling demo
Normalization GO Survival genefilter geneplotter affy vsn tilingArray affyio GO Survival
updated 17.2 years ago by ★ 13k • written 17.2 years ago by ★ 1.3k
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1
reply
2.8k
views
Displaying multiple survival curves on one graph
Survival graph Survival graph
updated 18.4 years ago by ★ 7.4k • written 18.4 years ago by ▴ 30
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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 ▴ 120 • written 16.7 years ago by ▴ 10
0
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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 65k • written 17.3 years ago by ▴ 320
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
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 Gordon Smyth 50k
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 by Gordon Smyth 50k
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? by James W. MacDonald 65k
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!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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