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 18 months ago by ★ 4.6k • written 18 months ago by ▴ 20
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
20 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 7.8 years ago by 67k • written 7.8 years ago by ▴ 20
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CEL file to expressionSet
affydata expressonset
updated 8.6 years ago by 67k • written 8.6 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 9.2 years ago by ★ 3.4k • written 9.2 years ago by • 0
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1
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2.3k
views
Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 14.6 years ago by 67k • written 14.6 years ago by ▴ 940
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1.1k
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getting original CEL files from Dilution
affydata affydata
updated 15.4 years ago by ★ 2.4k • written 15.4 years ago by ▴ 840
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.2 years ago Boel Brynedal ▴ 200
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2.0k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ★ 2.2k
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5
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2.1k
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 17.6 years ago by 67k • written 17.6 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
17.6 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
17.6 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 17.6 years ago by 67k • written 17.6 years ago by ▴ 450
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1.0k
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
17.7 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 17.8 years ago by 52k • written 17.8 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 17.9 years ago by 52k • written 17.9 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 17.9 years ago by 67k • written 17.9 years ago by ★ 2.2k
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8
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1.9k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 18.0 years ago by ★ 7.4k • written 18.0 years ago by ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
18.1 years ago Gordon Smyth 52k
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11
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3.0k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 18.1 years ago by ▴ 10 • written 18.1 years ago by ★ 2.2k
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10
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2.2k
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 18.2 years ago by ▴ 460 • written 18.2 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 18.2 years ago by 67k • written 18.2 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 18.2 years ago by ★ 5.5k • written 18.2 years ago by ▴ 460
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8
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2.3k
views
AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 18.2 years ago by ▴ 190 • written 18.2 years ago by ★ 2.9k
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1.3k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
18.3 years ago Martin Morgan 25k
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1.4k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 18.3 years ago by 25k • written 18.3 years ago by ★ 2.2k
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2
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1.3k
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"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 18.4 years ago by ★ 1.2k • written 18.4 years ago by ▴ 420
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1.1k
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.4 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
18.4 years ago k. brand ▴ 420
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980
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 18.5 years ago by 67k • written 18.5 years ago by ▴ 10
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
18.5 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 18.5 years ago by 67k • written 18.5 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 18.8 years ago by ▴ 70 • written 18.8 years ago by ★ 2.2k
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1.0k
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
19.1 years ago Jenny Drnevich ★ 2.2k
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969
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
19.5 years ago Gordon Smyth 52k
1
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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
19.5 years ago • updated 6 months ago Gordon Smyth 52k
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0
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1.1k
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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
19.6 years ago Naomi Altman ★ 6.0k
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2
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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 19.6 years ago by ★ 13k • written 19.6 years ago by 52k
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1
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1.3k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 20.6 years ago by ▴ 1000 • written 20.6 years ago by ▴ 60
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1
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1.2k
views
Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 21.4 years ago by 6.7k • written 21.4 years ago by ▴ 60
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1
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1.3k
views
Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 21.7 years ago by ★ 2.9k • written 21.7 years ago by ▴ 130
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3
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1.0k
views
Error loading reposTools
reposTools affy affydata reposTools affy affydata
21.7 years ago Warnes, Gregory R ▴ 460
42 results • Page 1 of 1
Recent ...
Replies
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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Popular Question to shepherl 4.1k
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