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 17 months ago by ★ 4.6k • written 17 months ago by ▴ 20
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
19 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 7.7 years ago by 67k • written 7.7 years ago by ▴ 20
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CEL file to expressionSet
affydata expressonset
updated 8.5 years ago by 67k • written 8.5 years ago by • 0
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5
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2.1k
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 9.1 years ago by ★ 3.4k • written 9.1 years ago by • 0
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2.3k
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 14.5 years ago by 67k • written 14.5 years ago by ▴ 940
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getting original CEL files from Dilution
affydata affydata
updated 15.3 years ago by ★ 2.4k • written 15.3 years ago by ▴ 840
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.1 years ago Boel Brynedal ▴ 200
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 17.3 years ago by ★ 7.4k • written 17.3 years ago by ★ 2.2k
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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 17.4 years ago by 67k • written 17.4 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
17.5 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
17.5 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 17.5 years ago by 67k • written 17.5 years ago by ▴ 450
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
17.6 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 17.7 years ago by 52k • written 17.7 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 17.8 years ago by 52k • written 17.8 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 17.8 years ago by 67k • written 17.8 years ago by ★ 2.2k
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oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
18.0 years ago Gordon Smyth 52k
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3.0k
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 18.0 years ago by ▴ 10 • written 18.0 years ago by ★ 2.2k
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10
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 18.1 years ago by ▴ 460 • written 18.1 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 18.1 years ago by 67k • written 18.1 years ago by ▴ 510
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12
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2.3k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 18.1 years ago by ★ 5.5k • written 18.1 years ago by ▴ 460
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AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 18.1 years ago by ▴ 190 • written 18.1 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
18.2 years ago Martin Morgan 25k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 18.2 years ago by 25k • written 18.2 years ago by ★ 2.2k
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"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 18.3 years ago by ★ 1.2k • written 18.3 years ago by ▴ 420
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.3 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
18.3 years ago k. brand ▴ 420
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967
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 18.4 years ago by 67k • written 18.4 years ago by ▴ 10
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
18.4 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 18.4 years ago by 67k • written 18.4 years ago by ▴ 160
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3
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1.6k
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error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 18.7 years ago by ▴ 70 • written 18.7 years ago by ★ 2.2k
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
19.0 years ago Jenny Drnevich ★ 2.2k
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960
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
19.4 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
19.4 years ago • updated 5 months ago Gordon Smyth 52k
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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
19.5 years ago Naomi Altman ★ 6.0k
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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 19.5 years ago by ★ 13k • written 19.5 years ago by 52k
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1.3k
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 20.5 years ago by ▴ 1000 • written 20.5 years ago by ▴ 60
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1.1k
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 21.3 years ago by 6.7k • written 21.3 years ago by ▴ 60
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1.3k
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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 21.5 years ago by ★ 2.9k • written 21.5 years ago by ▴ 130
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3
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1.0k
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Error loading reposTools
reposTools affy affydata reposTools affy affydata
21.6 years ago Warnes, Gregory R ▴ 460
42 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
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