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 4 months ago by ★ 3.6k • written 4 months ago by ▴ 10
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2
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289
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
7 months ago Susanna • 0
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1
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2.3k
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 6.6 years ago by 64k • written 6.6 years ago by ▴ 20
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866
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CEL file to expressionSet
affydata expressonset
updated 7.5 years ago by 64k • written 7.5 years ago by • 0
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5
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1.7k
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by • 0
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1
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2.1k
views
Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 13.4 years ago by 64k • written 13.4 years ago by ▴ 940
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926
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getting original CEL files from Dilution
affydata affydata
updated 14.3 years ago by ★ 2.4k • written 14.3 years ago by ▴ 840
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987
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
16.1 years ago Boel Brynedal ▴ 200
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7
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1.6k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 16.3 years ago by ★ 7.4k • written 16.3 years ago by ★ 2.2k
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5
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1.7k
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 16.4 years ago by 64k • written 16.4 years ago by ▴ 50
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928
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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
16.4 years ago Dave Jacoby ▴ 20
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852
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Fwd: limma gene symbol not avialable problem
Microarray Annotation Cancer cdf probe annotate affy affydata limma matchprobes affyio
16.5 years ago lidaof ▴ 450
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3
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1.2k
views
limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 16.5 years ago by 64k • written 16.5 years ago by ▴ 450
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783
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
16.6 years ago Yihuan Xu ▴ 130
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2
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1.5k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 16.7 years ago by 49k • written 16.7 years ago by ▴ 680
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972
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 16.7 years ago by 49k • written 16.7 years ago by ★ 2.2k
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1
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1.3k
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 16.7 years ago by 64k • written 16.7 years ago by ★ 2.2k
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8
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1.5k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 16.8 years ago by ★ 7.4k • written 16.8 years ago by ★ 2.2k
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1.1k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
16.9 years ago Gordon Smyth 49k
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11
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2.5k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.0 years ago by ▴ 10 • written 17.0 years ago by ★ 2.2k
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10
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1.7k
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 17.0 years ago by ▴ 460 • written 17.0 years ago by ▴ 70
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1
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2.6k
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 17.0 years ago by 64k • written 17.0 years ago by ▴ 510
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12
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1.8k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.0 years ago by ★ 5.5k • written 17.0 years ago by ▴ 460
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8
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1.8k
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AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 17.1 years ago by ▴ 190 • written 17.1 years ago by ★ 2.9k
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1.1k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
17.1 years ago Martin Morgan 25k
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4
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1.1k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 17.1 years ago by 25k • written 17.1 years ago by ★ 2.2k
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2
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1.0k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 17.2 years ago by ★ 1.2k • written 17.2 years ago by ▴ 420
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878
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
17.2 years ago k. brand ▴ 420
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850
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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
17.2 years ago k. brand ▴ 420
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824
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 17.3 years ago by 64k • written 17.3 years ago by ▴ 10
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2
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1.4k
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
17.3 years ago Jenny Drnevich ★ 2.2k
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980
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qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 17.4 years ago by 64k • written 17.4 years ago by ▴ 160
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3
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1.3k
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error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 17.7 years ago by ▴ 70 • written 17.7 years ago by ★ 2.2k
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843
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
18.0 years ago Jenny Drnevich ★ 2.2k
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
18.4 years ago Gordon Smyth 49k
1
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1
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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
18.4 years ago Gordon Smyth 49k
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0
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847
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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
18.5 years ago Naomi Altman ★ 6.0k
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2
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1.2k
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 18.5 years ago by 13k • written 18.5 years ago by 49k
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1.0k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 19.4 years ago by ▴ 1000 • written 19.4 years ago by ▴ 60
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930
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 20.2 years ago by 6.7k • written 20.2 years ago by ▴ 60
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1.0k
views
Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 20.5 years ago by ★ 2.9k • written 20.5 years ago by ▴ 130
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3
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776
views
Error loading reposTools
reposTools affy affydata reposTools affy affydata
20.6 years ago Warnes, Gregory R ▴ 460
42 results • Page 1 of 1
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Comment: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)? No, you should not apply any batch correction before …
Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
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Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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