Showing : gcrma • reset
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Question about patchwork affy pre-processing
Normalization affy gcrma Normalization affy gcrma
updated 18.6 years ago by ★ 1.2k • written 18.6 years ago by ▴ 10
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6
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2.5k
views
ReadAffy Error: new versions causing problems?
genefilter gcrma matchprobes simpleaffy affyio genefilter gcrma matchprobes simpleaffy
updated 18.6 years ago by ▴ 20 • written 18.7 years ago by ▴ 200
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9
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2.6k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 18.7 years ago by ★ 7.4k • written 18.7 years ago by ★ 2.2k
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0
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1.3k
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Ranking genes according to tissue specificity
probe affy gcrma probe affy gcrma
18.8 years ago Cei Abreu-Goodger ▴ 830
0
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1
reply
784
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error getting CDF
cdf gcrma cdf gcrma
updated 18.8 years ago by 68k • written 18.8 years ago by ▴ 20
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1
reply
1.1k
views
Format NCprobe index file gcrma
gcrma gcrma
updated 18.8 years ago by ▴ 200 • written 18.8 years ago by ▴ 30
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1
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1.4k
views
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
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1.1k
views
gcrma and chip without mm values
probe gcrma probe gcrma
updated 18.9 years ago by ▴ 200 • written 18.9 years ago by ▴ 10
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1
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1.5k
views
annaffy errors
GO Survival mgu74av2 cdf annotate affy limma gcrma matchprobes annaffy simpleaffy plier
updated 19.0 years ago by 68k • written 19.0 years ago by ▴ 320
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1
reply
1.3k
views
gcrma and chip without mm values
probe gcrma probe gcrma
updated 19.0 years ago by 68k • written 19.0 years ago by ▴ 80
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0
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931
views
Bioconductor Digest, Vol 47, Issue 26
GO cdf probe affy gcrma PROcess convert GO cdf probe affy gcrma PROcess convert
19.0 years ago Manhong Dai ▴ 200
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2
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1.2k
views
Loading multiple Affy chips simultaneously
GO cdf gcrma GO cdf gcrma
19.0 years ago Paul Boutros ▴ 340
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4
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2.0k
views
Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 19.0 years ago by ▴ 550 • written 19.0 years ago by ▴ 350
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0
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857
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[Bioc] Removing outlier/masked probes and gcRMA
cdf affy gcrma cdf affy gcrma
19.0 years ago Amy Mikhail ▴ 460
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4
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1.7k
views
gcrma with bpmap file instead of cdf file
cdf gcrma cdf gcrma
19.0 years ago Baoqiang Cao ▴ 30
0
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4
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1.7k
views
How to read and normalize hundreds of CEL files?
Microarray gcrma Microarray gcrma
updated 19.1 years ago by ▴ 820 • written 19.1 years ago by ▴ 80
0
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11
replies
3.5k
views
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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3
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1.9k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 19.1 years ago by ★ 13k • written 19.1 years ago by ▴ 510
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4
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1.3k
views
GCRMA with HG-U95A and HG-U95Av2
Normalization cdf gcrma Normalization cdf gcrma
updated 19.1 years ago by ★ 7.4k • written 19.1 years ago by ▴ 10
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3
replies
1.7k
views
How to use detect call in GCRMA (or RMA) analysis?
gcrma gcrma
updated 19.1 years ago by ▴ 890 • written 19.1 years ago by ▴ 10
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4
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1.6k
views
gcrma background correction
cdf gcrma matchprobes cdf gcrma matchprobes
updated 19.1 years ago by ★ 6.5k • written 19.1 years ago by ▴ 170
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0
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725
views
Trouble with gcrma background correction
cdf gcrma cdf gcrma
19.1 years ago Hervé Pagès 16k
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10
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2.2k
views
problems with gcrma just.gcrma
mgu74av2 affy gcrma mgu74av2 affy gcrma
19.1 years ago Elisabetta Manduchi ▴ 160
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10
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2.7k
views
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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2
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1.4k
views
2fold sigchanges from limma
GO Survival hgu133a2 annotate hexbin limma gcrma matchprobes annaffy GO Survival hexbin
updated 19.1 years ago by 53k • written 19.1 years ago by ▴ 60
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12
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2.8k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 19.1 years ago by ★ 5.5k • written 19.1 years ago by ▴ 460
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2
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1.1k
views
trouble with gcrma: bgcorrection
cdf gcrma cdf gcrma
updated 19.1 years ago by ▴ 200 • written 19.2 years ago by ▴ 170
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2
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3.4k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 19.2 years ago by ★ 7.4k • written 19.2 years ago by ▴ 360
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2
replies
1.3k
views
Trouble with gcrma background correction
gcrma gcrma
updated 19.2 years ago by 16k • written 19.2 years ago by ▴ 170
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2
replies
1.4k
views
trouble with gcrma background correction
gcrma gcrma
updated 19.2 years ago by ▴ 200 • written 19.2 years ago by ▴ 170
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1
reply
1.1k
views
gcrma on PM-only Affy data
probe affy gcrma probe affy gcrma
updated 19.2 years ago by ▴ 200 • written 19.2 years ago by ★ 2.2k
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1
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1.5k
views
warning from make.cdf.package - FYI
GO Survival cdf Biobase annotate genefilter graph makecdfenv limma gcrma matchprobes GO
updated 19.2 years ago by 68k • written 19.2 years ago by ★ 2.2k
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0
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1.0k
views
still having problems reading *nonbinary.CEL.gz absolute path in a file
Microarray gcrma Microarray gcrma
19.2 years ago D.Enrique ESCOBAR ESPINOZA ▴ 360
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1
reply
822
views
expression levels of individual probes
gcrma gcrma
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 10
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0
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1.5k
views
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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1
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1.1k
views
Normalisation GCRMA Error
gcrma gcrma
updated 19.3 years ago by ★ 1.2k • written 19.3 years ago by ▴ 260
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0
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687
views
FW: create probe file from CDF?
Genetics Cancer cdf probe gcrma Genetics Cancer cdf probe gcrma
19.3 years ago Lo, Ken ▴ 50
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2
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1.6k
views
"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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0
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1.2k
views
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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2
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1.3k
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 19.3 years ago by ★ 6.5k • written 19.3 years ago by ▴ 420
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1
reply
978
views
cdf for ATH1 array
cdf gcrma cdf gcrma
updated 19.3 years ago by 68k • written 19.4 years ago by ▴ 10
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0
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1.2k
views
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
0
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1
reply
780
views
Affy High Throughput arrays
cdf probe affy gcrma cdf probe affy gcrma
updated 19.4 years ago by 68k • written 19.4 years ago by ▴ 10
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1
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775
views
GCRMA Bayes theory question
gcrma gcrma
updated 19.4 years ago by ★ 2.0k • written 19.4 years ago by ▴ 10
0
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5
replies
2.4k
views
RMA and justRMA error
Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio
19.4 years ago Aedin Culhane ▴ 510
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1
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1.6k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 19.4 years ago by ★ 7.4k • written 19.4 years ago by ★ 2.2k
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2
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1.9k
views
problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
19.4 years ago Jenny Drnevich ★ 2.2k
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2
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1.4k
views
just.gcrma and normalisation
Genetics affy gcrma Genetics affy gcrma
updated 19.6 years ago by ▴ 200 • written 19.6 years ago by ▴ 310
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2
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1.3k
views
vector allocation error
hgu133plus2 gcrma hgu133plus2 gcrma
updated 19.6 years ago by ▴ 60 • written 19.6 years ago by ▴ 50
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0
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1.2k
views
W: unnormalised vs normalised distribution
Cancer gcrma PICS Cancer gcrma PICS
19.6 years ago Benjamin Otto ▴ 830
406 results • Page 4 of 9
Recent ...
Replies
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…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
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
Comment: Question about the filterByExpr function inputs in edgeR
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