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 19 months ago by ★ 4.7k • written 19 months ago by ▴ 20
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
22 months ago • updated 21 months ago Susanna • 0
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2.9k
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 20
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CEL file to expressionSet
affydata expressonset
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
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5
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2.2k
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 9.3 years ago by ★ 3.4k • written 9.3 years ago by • 0
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1
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2.3k
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 14.7 years ago by 68k • written 14.7 years ago by ▴ 950
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1.1k
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getting original CEL files from Dilution
affydata affydata
updated 15.5 years ago by ★ 2.4k • written 15.5 years ago by ▴ 840
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.3 years ago Boel Brynedal ▴ 200
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2.0k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 17.5 years ago by ★ 7.4k • written 17.5 years ago by ★ 2.2k
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5
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2.1k
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 17.6 years ago by 68k • written 17.6 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
17.7 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
17.7 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 17.7 years ago by 68k • written 17.7 years ago by ▴ 450
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1.0k
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
17.8 years ago Yihuan Xu ▴ 130
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1.9k
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.9 years ago by 52k • written 17.9 years ago by ▴ 680
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1.2k
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 17.9 years ago by 52k • written 17.9 years ago by ★ 2.2k
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1.5k
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 17.9 years ago by 68k • written 17.9 years ago by ★ 2.2k
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8
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2.0k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 18.1 years ago by ★ 7.4k • written 18.1 years ago by ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
18.2 years ago Gordon Smyth 52k
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11
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3.0k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 18.2 years ago by ▴ 10 • written 18.2 years ago by ★ 2.2k
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10
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2.3k
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 18.3 years ago by ▴ 460 • written 18.3 years ago by ▴ 70
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3.0k
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 18.3 years ago by 68k • written 18.3 years ago by ▴ 510
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12
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2.4k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 18.3 years ago by ★ 5.5k • written 18.3 years ago by ▴ 460
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8
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2.3k
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AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 18.3 years ago by ▴ 190 • written 18.3 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
18.3 years ago Martin Morgan 25k
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1.4k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 18.4 years ago by 25k • written 18.4 years ago by ★ 2.2k
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2
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1.4k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 18.5 years ago by ★ 1.2k • written 18.5 years ago by ▴ 420
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1.1k
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.5 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
18.5 years ago k. brand ▴ 420
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990
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 18.6 years ago by 68k • written 18.6 years ago by ▴ 10
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
18.6 years ago Jenny Drnevich ★ 2.2k
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1.2k
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qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 18.6 years ago by 68k • written 18.6 years ago by ▴ 160
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3
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1.7k
views
error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 18.9 years ago by ▴ 70 • written 18.9 years ago by ★ 2.2k
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1.0k
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
19.2 years ago Jenny Drnevich ★ 2.2k
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988
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
19.6 years ago Gordon Smyth 52k
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1.4k
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A question about paired data and how to set up the designmatrix in LIMMA
limma affydata
19.6 years ago • updated 7 months ago Gordon Smyth 52k
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0
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1.1k
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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
19.7 years ago Naomi Altman ★ 6.0k
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2
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1.5k
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 19.7 years ago by ★ 13k • written 19.7 years ago by 52k
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1
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1.3k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 20.6 years ago by ▴ 1000 • written 20.6 years ago by ▴ 60
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1
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1.2k
views
Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 21.4 years ago by 6.7k • written 21.4 years ago by ▴ 60
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1
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1.3k
views
Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 21.7 years ago by ★ 2.9k • written 21.7 years ago by ▴ 130
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3
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1.1k
views
Error loading reposTools
reposTools affy affydata reposTools affy affydata
21.8 years ago Warnes, Gregory R ▴ 460
42 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
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