Showing : affydata • reset
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Affymetrix hgu133plus2.db: How to best derive an expression value for genes that map to multiple probe ids
affydata hgu133plus2.db AffymetrixChip
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
2.7 years ago Susanna • 0
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3.2k
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 20
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CEL file to expressionSet
affydata expressonset
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
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2.6k
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by • 0
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1
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2.5k
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 15.6 years ago by 68k • written 15.6 years ago by ▴ 950
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getting original CEL files from Dilution
affydata affydata
updated 16.4 years ago by ★ 2.4k • written 16.4 years ago by ▴ 840
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
18.2 years ago Boel Brynedal ▴ 200
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 18.4 years ago by ★ 7.4k • written 18.4 years ago by ★ 2.2k
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5
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 18.5 years ago by 68k • written 18.5 years ago by ▴ 50
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Return of "I'm sorry, I do not know about chip type (foo)"
Survival cdf affydata limma gcrma matchprobes affyPLM simpleaffy Survival cdf affydata
18.5 years ago Dave Jacoby ▴ 20
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Fwd: limma gene symbol not avialable problem
Microarray Annotation Cancer cdf probe annotate affy affydata limma matchprobes affyio
18.6 years ago lidaof ▴ 450
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limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 18.6 years ago by 68k • written 18.6 years ago by ▴ 450
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
18.7 years ago Yihuan Xu ▴ 130
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2.2k
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 18.8 years ago by 53k • written 18.8 years ago by ▴ 680
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1.4k
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 18.8 years ago by 53k • written 18.8 years ago by ★ 2.2k
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1.7k
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 18.8 years ago by 68k • written 18.8 years ago by ★ 2.2k
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8
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2.4k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
19.1 years ago Gordon Smyth 53k
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11
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3.5k
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 19.1 years ago by ▴ 10 • written 19.1 years ago by ★ 2.2k
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10
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2.7k
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 19.1 years ago by ▴ 460 • written 19.1 years ago by ▴ 70
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 19.1 years ago by 68k • written 19.1 years ago by ▴ 510
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12
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2.8k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 19.2 years ago by ★ 5.5k • written 19.1 years ago by ▴ 460
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8
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AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 19.2 years ago by ▴ 190 • written 19.2 years ago by ★ 2.9k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
19.2 years ago Martin Morgan 25k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 19.2 years ago by 25k • written 19.2 years ago by ★ 2.2k
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2
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1.6k
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"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 19.3 years ago by ★ 1.2k • written 19.3 years ago by ▴ 420
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
19.3 years ago k. brand ▴ 420
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4 replicates, of 3 tissues- one good hyb (2xreps), one bad hyb (2xreps). Best way forward?
qPCR affy affydata vsn limma gcrma matchprobes affyPLM affyio BRAIN qPCR affy affydata
19.4 years ago k. brand ▴ 420
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1.1k
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 19.4 years ago by 68k • written 19.4 years ago by ▴ 10
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1.9k
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
19.5 years ago Jenny Drnevich ★ 2.2k
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1.3k
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qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 19.5 years ago by 68k • written 19.5 years ago by ▴ 160
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3
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1.9k
views
error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 19.8 years ago by ▴ 70 • written 19.8 years ago by ★ 2.2k
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
20.1 years ago Jenny Drnevich ★ 2.2k
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1.1k
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
20.5 years ago Gordon Smyth 53k
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1
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1.6k
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A question about paired data and how to set up the designmatrix in LIMMA
limma affydata
20.5 years ago • updated 18 months ago Gordon Smyth 53k
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differences or 1-channel (was Re: Agilent Arrays)
Normalization GO probe affy affydata vsn limma marray BEAT Normalization GO probe affy
20.6 years ago Naomi Altman ★ 6.0k
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1.7k
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 20.6 years ago by ★ 13k • written 20.6 years ago by 53k
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1.6k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 21.5 years ago by ▴ 1000 • written 21.5 years ago by ▴ 60
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1
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1.4k
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 22.3 years ago by 6.7k • written 22.3 years ago by ▴ 60
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1.5k
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Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 22.6 years ago by ★ 2.9k • written 22.6 years ago by ▴ 130
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3
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1.3k
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Error loading reposTools
reposTools affy affydata reposTools affy affydata
22.7 years ago Warnes, Gregory R ▴ 460
42 results • Page 1 of 1
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Comment: Pairwise comparison of multiple groups with different base by ja569116 • 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
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…
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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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