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A question about paired data and how to set up the designmatrix in LIMMA
affydata limma affydata limma
18.8 years ago Gordon Smyth 50k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
17.5 years ago Martin Morgan 25k
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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 17.4 years ago by ▴ 190 • written 17.4 years ago by ★ 2.9k
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Error loading reposTools
reposTools affy affydata reposTools affy affydata
21.0 years ago Warnes, Gregory R ▴ 460
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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 20.9 years ago by ★ 2.9k • written 20.9 years ago by ▴ 130
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 20.6 years ago by 6.7k • written 20.6 years ago by ▴ 60
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 19.8 years ago by ▴ 1000 • written 19.8 years ago by ▴ 60
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2
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 18.8 years ago by ★ 13k • written 18.8 years ago by 50k
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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
18.8 years ago Naomi Altman ★ 6.0k
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
18.8 years ago Gordon Smyth 50k
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0
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901
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
18.4 years ago Jenny Drnevich ★ 2.2k
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3
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1.4k
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error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 18.0 years ago by ▴ 70 • written 18.0 years ago by ★ 2.2k
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qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 17.8 years ago by 65k • written 17.8 years ago by ▴ 160
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2
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1.5k
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
17.7 years ago Jenny Drnevich ★ 2.2k
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1
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875
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 17.7 years ago by 65k • written 17.7 years ago by ▴ 10
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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
17.6 years ago k. brand ▴ 420
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959
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
17.6 years ago k. brand ▴ 420
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"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 17.6 years ago by ★ 1.2k • written 17.6 years ago by ▴ 420
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4
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 17.5 years ago by 25k • written 17.5 years ago by ★ 2.2k
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12
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1.9k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 460
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 17.4 years ago by 65k • written 17.4 years ago by ▴ 510
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10
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 17.4 years ago by ▴ 460 • written 17.4 years ago by ▴ 70
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11
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2.7k
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.4 years ago by ▴ 10 • written 17.4 years ago by ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
17.3 years ago Gordon Smyth 50k
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8
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1.6k
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oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 17.2 years ago by ★ 7.4k • written 17.2 years ago by ★ 2.2k
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1
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1.1k
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 17.1 years ago by 50k • written 17.1 years ago by ★ 2.2k
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1
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1.4k
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
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2
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1.6k
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.1 years ago by 50k • written 17.1 years ago by ▴ 680
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849
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
16.9 years ago Yihuan Xu ▴ 130
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3
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1.3k
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limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 16.9 years ago by 65k • written 16.9 years ago by ▴ 450
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Fwd: limma gene symbol not avialable problem
Microarray Annotation Cancer cdf probe annotate affy affydata limma matchprobes affyio
16.9 years ago lidaof ▴ 450
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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
16.8 years ago Dave Jacoby ▴ 20
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5
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1.9k
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 16.8 years ago by 65k • written 16.8 years ago by ▴ 50
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7
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1.7k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 16.6 years ago by ★ 7.4k • written 16.6 years ago by ★ 2.2k
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1.1k
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
16.5 years ago Boel Brynedal ▴ 200
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1
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990
views
getting original CEL files from Dilution
affydata affydata
updated 14.7 years ago by ★ 2.4k • written 14.7 years ago by ▴ 840
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1
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2.2k
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 13.8 years ago by 65k • written 13.8 years ago by ▴ 940
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5
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1.9k
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 8.4 years ago by ★ 3.3k • written 8.4 years ago by • 0
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1
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922
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CEL file to expressionSet
affydata expressonset
updated 7.8 years ago by 65k • written 7.8 years ago by • 0
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1
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2.5k
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 20
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2
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396
views
justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
11 months ago Susanna • 0
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1
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468
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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 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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