Showing : affydata • reset
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A question about paired data and how to set up the designmatrix in LIMMA
affydata limma affydata limma
16.8 years ago Gordon Smyth 45k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
15.6 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 15.5 years ago by ▴ 170 • written 15.5 years ago by ★ 2.9k
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Error loading reposTools
reposTools affy affydata reposTools affy affydata
19.0 years ago Warnes, Gregory R ▴ 460
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744
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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 19.0 years ago by ★ 2.9k • written 19.0 years ago by ▴ 130
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 18.7 years ago by 6.6k • written 18.7 years ago by ▴ 60
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 17.9 years ago by ▴ 1000 • written 17.9 years ago by ▴ 60
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2
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703
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 16.9 years ago by 13k • written 16.9 years ago by 45k
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628
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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
16.9 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
16.8 years ago Gordon Smyth 45k
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0
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606
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
16.4 years ago Jenny Drnevich ★ 2.2k
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3
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error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 16.1 years ago by ▴ 70 • written 16.1 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 15.8 years ago by 59k • written 15.8 years ago by ▴ 160
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888
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
15.8 years ago Jenny Drnevich ★ 2.2k
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645
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 15.8 years ago by 59k • written 15.8 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
15.7 years ago k. brand ▴ 420
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609
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
15.7 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 15.7 years ago by ★ 1.2k • written 15.7 years ago by ▴ 420
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4
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840
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 15.6 years ago by 25k • written 15.6 years ago by ★ 2.2k
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12
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1.1k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ▴ 460
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1
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2.0k
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 15.5 years ago by 59k • written 15.5 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 15.5 years ago by ▴ 460 • written 15.5 years ago by ▴ 70
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11
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1.9k
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 15.4 years ago by ▴ 10 • written 15.4 years ago by ★ 2.2k
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825
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
15.4 years ago Gordon Smyth 45k
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8
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oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 15.3 years ago by ★ 7.4k • written 15.3 years ago by ★ 2.2k
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699
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 15.2 years ago by 45k • written 15.2 years ago by ★ 2.2k
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1
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948
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 15.2 years ago by 59k • written 15.2 years ago by ★ 2.2k
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2
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1.1k
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 15.1 years ago by 45k • written 15.1 years ago by ▴ 680
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584
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
15.0 years ago Yihuan Xu ▴ 130
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3
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901
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limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 14.9 years ago by 59k • written 14.9 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
14.9 years ago lidaof ▴ 450
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0
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698
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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
14.9 years ago Dave Jacoby ▴ 20
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5
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 14.9 years ago by 59k • written 14.9 years ago by ▴ 50
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7
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1.1k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 14.7 years ago by ★ 7.4k • written 14.7 years ago by ★ 2.2k
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690
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
14.5 years ago Boel Brynedal ▴ 200
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1
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709
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getting original CEL files from Dilution
affydata affydata
updated 12.7 years ago by ★ 2.4k • written 12.7 years ago by ▴ 840
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1
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1.8k
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 11.9 years ago by 59k • written 11.9 years ago by ▴ 940
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5
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 6.5 years ago by ★ 2.8k • written 6.5 years ago by • 0
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694
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CEL file to expressionSet
affydata expressonset
updated 5.9 years ago by 59k • written 5.9 years ago by • 0
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1.7k
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 5.1 years ago by 59k • written 5.1 years ago by ▴ 20
40 results • Page 1 of 1
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Answer: help understanding limma by Gordon Smyth 45k
It is obvious that you haven't exported and read the correct intensity data, as you admit yourself in your question. I don't know what the …
Answer: performing the differential binding in ChIP-seq by etiennedanis • 0
DiffBind https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Hi Michael, thanks for your reply. One more question. If the qvalue (and pvalue) for all DTEs are the same, the Volcano plot will look lik…
Comment: R: problem with running time-series analysis software: Mfuzz by soda ▴ 80
I have solved this problem by myself. My data.frame is not suitable for Mfuzz.
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Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
C: DESeq2 - Differences between plotCounts and normalized counts
C: DESEq2 - Change reference level change "Contrasts" results
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