Showing : gcRMA • reset
0
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3
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Question about patchwork affy pre-processing
Normalization affy gcrma Normalization affy gcrma
updated 18.4 years ago by ★ 1.2k • written 18.4 years ago by ▴ 10
0
votes
6
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2.4k
views
ReadAffy Error: new versions causing problems?
genefilter gcrma matchprobes simpleaffy affyio genefilter gcrma matchprobes simpleaffy
updated 18.5 years ago by ▴ 20 • written 18.5 years ago by ▴ 200
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9
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2.5k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ★ 2.2k
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0
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1.3k
views
Ranking genes according to tissue specificity
probe affy gcrma probe affy gcrma
18.6 years ago Cei Abreu-Goodger ▴ 830
0
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1
reply
769
views
error getting CDF
cdf gcrma cdf gcrma
updated 18.6 years ago by 68k • written 18.6 years ago by ▴ 20
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1
reply
1.1k
views
Format NCprobe index file gcrma
gcrma gcrma
updated 18.6 years ago by ▴ 200 • written 18.6 years ago by ▴ 30
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1
reply
1.3k
views
topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 18.6 years ago by 53k • written 18.6 years ago by ★ 2.2k
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1
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1.0k
views
gcrma and chip without mm values
probe gcrma probe gcrma
updated 18.7 years ago by ▴ 200 • written 18.7 years ago by ▴ 10
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1
reply
1.5k
views
annaffy errors
GO Survival mgu74av2 cdf annotate affy limma gcrma matchprobes annaffy simpleaffy plier
updated 18.8 years ago by 68k • written 18.8 years ago by ▴ 320
0
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1
reply
1.3k
views
gcrma and chip without mm values
probe gcrma probe gcrma
updated 18.8 years ago by 68k • written 18.8 years ago by ▴ 80
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0
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891
views
Bioconductor Digest, Vol 47, Issue 26
GO cdf probe affy gcrma PROcess convert GO cdf probe affy gcrma PROcess convert
18.8 years ago Manhong Dai ▴ 200
0
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2
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1.1k
views
Loading multiple Affy chips simultaneously
GO cdf gcrma GO cdf gcrma
18.8 years ago Paul Boutros ▴ 340
0
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4
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1.9k
views
Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 18.8 years ago by ▴ 550 • written 18.8 years ago by ▴ 350
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0
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832
views
[Bioc] Removing outlier/masked probes and gcRMA
cdf affy gcrma cdf affy gcrma
18.8 years ago Amy Mikhail ▴ 460
0
votes
4
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1.6k
views
gcrma with bpmap file instead of cdf file
cdf gcrma cdf gcrma
18.8 years ago Baoqiang Cao ▴ 30
0
votes
4
replies
1.6k
views
How to read and normalize hundreds of CEL files?
Microarray gcrma Microarray gcrma
updated 18.9 years ago by ▴ 820 • written 18.9 years ago by ▴ 80
0
votes
11
replies
3.4k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 18.9 years ago by ▴ 10 • written 18.9 years ago by ★ 2.2k
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votes
3
replies
1.9k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 18.9 years ago by ★ 13k • written 18.9 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 18.9 years ago by ★ 7.4k • written 18.9 years ago by ▴ 10
0
votes
3
replies
1.6k
views
How to use detect call in GCRMA (or RMA) analysis?
gcrma gcrma
updated 18.9 years ago by ▴ 890 • written 18.9 years ago by ▴ 10
0
votes
4
replies
1.5k
views
gcrma background correction
cdf gcrma matchprobes cdf gcrma matchprobes
updated 18.9 years ago by ★ 6.5k • written 18.9 years ago by ▴ 170
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0
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698
views
Trouble with gcrma background correction
cdf gcrma cdf gcrma
18.9 years ago Hervé Pagès 16k
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10
replies
2.1k
views
problems with gcrma just.gcrma
mgu74av2 affy gcrma mgu74av2 affy gcrma
18.9 years ago Elisabetta Manduchi ▴ 160
0
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10
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2.6k
views
Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 18.9 years ago by ▴ 460 • written 19.0 years ago by ▴ 70
0
votes
2
replies
1.4k
views
2fold sigchanges from limma
GO Survival hgu133a2 annotate hexbin limma gcrma matchprobes annaffy GO Survival hexbin
updated 18.9 years ago by 53k • written 18.9 years ago by ▴ 60
0
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12
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2.7k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 19.0 years ago by ★ 5.5k • written 19.0 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 19.0 years ago by ▴ 200 • written 19.0 years ago by ▴ 170
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2
replies
3.4k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ▴ 360
0
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2
replies
1.2k
views
Trouble with gcrma background correction
gcrma gcrma
updated 19.0 years ago by 16k • written 19.0 years ago by ▴ 170
0
votes
2
replies
1.3k
views
trouble with gcrma background correction
gcrma gcrma
updated 19.0 years ago by ▴ 200 • written 19.0 years ago by ▴ 170
0
votes
1
reply
1.1k
views
gcrma on PM-only Affy data
probe affy gcrma probe affy gcrma
updated 19.0 years ago by ▴ 200 • written 19.0 years ago by ★ 2.2k
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1
reply
1.5k
views
warning from make.cdf.package - FYI
GO Survival cdf Biobase annotate genefilter graph makecdfenv limma gcrma matchprobes GO
updated 19.0 years ago by 68k • written 19.0 years ago by ★ 2.2k
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0
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985
views
still having problems reading *nonbinary.CEL.gz absolute path in a file
Microarray gcrma Microarray gcrma
19.0 years ago D.Enrique ESCOBAR ESPINOZA ▴ 360
0
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1
reply
792
views
expression levels of individual probes
gcrma gcrma
updated 19.0 years ago by 68k • written 19.0 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
19.0 years ago Martin Morgan 25k
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1
reply
1.1k
views
Normalisation GCRMA Error
gcrma gcrma
updated 19.1 years ago by ★ 1.2k • written 19.1 years ago by ▴ 260
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0
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665
views
FW: create probe file from CDF?
Genetics Cancer cdf probe gcrma Genetics Cancer cdf probe gcrma
19.1 years ago Lo, Ken ▴ 50
0
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2
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1.5k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 19.1 years ago by ★ 1.2k • written 19.1 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
19.2 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 19.2 years ago by ★ 6.5k • written 19.2 years ago by ▴ 420
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votes
1
reply
950
views
cdf for ATH1 array
cdf gcrma cdf gcrma
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 10
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0
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1.2k
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
19.2 years ago k. brand ▴ 420
0
votes
1
reply
761
views
Affy High Throughput arrays
cdf probe affy gcrma cdf probe affy gcrma
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 10
0
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1
reply
740
views
GCRMA Bayes theory question
gcrma gcrma
updated 19.2 years ago by ★ 2.0k • written 19.2 years ago by ▴ 10
0
votes
5
replies
2.3k
views
RMA and justRMA error
Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio
19.2 years ago Aedin Culhane ▴ 510
0
votes
1
reply
1.5k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 19.3 years ago by ★ 7.4k • written 19.3 years ago by ★ 2.2k
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votes
2
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1.8k
views
problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
19.3 years ago Jenny Drnevich ★ 2.2k
0
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2
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1.4k
views
just.gcrma and normalisation
Genetics affy gcrma Genetics affy gcrma
updated 19.4 years ago by ▴ 200 • written 19.4 years ago by ▴ 310
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votes
2
replies
1.2k
views
vector allocation error
hgu133plus2 gcrma hgu133plus2 gcrma
updated 19.4 years ago by ▴ 60 • written 19.4 years ago by ▴ 50
0
votes
0
replies
1.1k
views
W: unnormalised vs normalised distribution
Cancer gcrma PICS Cancer gcrma PICS
19.4 years ago Benjamin Otto ▴ 830
406 results • Page 4 of 9
Recent ...
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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