Showing : affydata • reset
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 18.4 years ago by ★ 5.5k • written 18.4 years ago by ▴ 460
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 18.4 years ago by ▴ 10 • written 18.4 years ago by ★ 2.2k
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Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 18.4 years ago by ▴ 460 • written 18.4 years ago by ▴ 70
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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 18.4 years ago by ▴ 190 • written 18.4 years ago by ★ 2.9k
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oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 18.2 years ago by ★ 7.4k • written 18.2 years ago by ★ 2.2k
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problem with GOstats, developmental version?
GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO
updated 17.6 years ago by ★ 7.4k • written 17.7 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 17.8 years ago by 68k • written 17.8 years ago by ▴ 50
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collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 9.4 years ago by ★ 3.4k • written 9.4 years ago by • 0
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 18.5 years ago by 25k • written 18.5 years ago by ★ 2.2k
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3
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limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 17.9 years ago by 68k • written 17.9 years ago by ▴ 450
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error in mas5calls() for soybean chip
Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4
updated 19.0 years ago by ▴ 70 • written 19.0 years ago by ★ 2.2k
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Error loading reposTools
reposTools affy affydata reposTools affy affydata
22.0 years ago Warnes, Gregory R ▴ 460
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2
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 18.1 years ago by 52k • written 18.1 years ago by ▴ 680
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Bioconductor Digest, Vol 28, Issue 23
Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata
updated 19.8 years ago by ★ 13k • written 19.8 years ago by 52k
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problem loading affycoretools
Survival hgu95av2 Biobase Ruuid annotate genefilter multtest affydata graph limma gcrma
18.7 years ago Jenny Drnevich ★ 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 18.6 years ago by ★ 1.2k • written 18.6 years ago by ▴ 420
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justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore hthgu133a.db affydata
23 months ago Susanna • 0
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 20.8 years ago by ▴ 1000 • written 20.8 years ago by ▴ 60
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Querying PubMed Database
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata
updated 21.6 years ago by 6.7k • written 21.6 years ago by ▴ 60
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 18.7 years ago by 68k • written 18.7 years ago by ▴ 10
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getting original CEL files from Dilution
affydata affydata
updated 15.7 years ago by ★ 2.4k • written 15.7 years ago by ▴ 840
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Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 14.8 years ago by 68k • written 14.8 years ago by ▴ 950
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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 21.9 years ago by ★ 2.9k • written 21.9 years ago by ▴ 130
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CEL file to expressionSet
affydata expressonset
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
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Reading sub-selected CEL files in R using ReadAffy()
Affy affydata
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 20
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967
views
Affymetrix hgu133plus2.db: How to best derive an expression value for genes that map to multiple probe ids
affydata hgu133plus2.db AffymetrixChip
updated 21 months ago by ★ 4.8k • written 21 months ago by ▴ 20
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3.1k
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ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 18.4 years ago by 68k • written 18.4 years ago by ▴ 510
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A question about paired data and how to set up the designmatrix in LIMMA
limma affydata
19.8 years ago • updated 9 months ago Gordon Smyth 52k
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1
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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 18.8 years ago by 68k • written 18.8 years ago by ▴ 160
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1.3k
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topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 18.1 years ago by 52k • written 18.1 years ago by ★ 2.2k
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question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 18.1 years ago by 68k • written 18.1 years ago by ★ 2.2k
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Fwd: limma gene symbol not avialable problem
Microarray Annotation Cancer cdf probe annotate affy affydata limma matchprobes affyio
17.9 years ago lidaof ▴ 450
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
19.4 years ago Jenny Drnevich ★ 2.2k
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flagging spots in marray
aCGH Microarray Normalization GO Cancer Biobase annotate genefilter affy affydata limma
18.3 years ago Gordon Smyth 52k
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A question about paired data and how to set up the designmatrix in LIMMA]
affydata limma affydata limma
19.8 years ago Gordon Smyth 52k
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0
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
18.5 years ago Martin Morgan 25k
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simpleaffy problem - drosophila2
drosophila2 cdf affy affydata simpleaffy drosophila2 cdf affy affydata simpleaffy
17.9 years ago Yihuan Xu ▴ 130
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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
19.8 years ago Naomi Altman ★ 6.0k
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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
18.6 years ago k. brand ▴ 420
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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
17.8 years ago Dave Jacoby ▴ 20
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.5 years ago Boel Brynedal ▴ 200
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.6 years ago k. brand ▴ 420
42 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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