Showing : geneplotter • reset
6
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 10
0
votes
1
reply
2.0k
views
install geneplotter
geneplotter geneplotter
updated 11.2 years ago by 68k • written 11.2 years ago by ★ 13k
0
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0
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1.9k
views
library(\"geneplotter\") fails on load
GO hgu95av2 geneplotter GO hgu95av2 geneplotter
11.8 years ago Guest User ★ 13k
0
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0
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1.2k
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geneplotter - buildChromLoc for arrays with no .db
GO geneplotter GO geneplotter
12.2 years ago Lavinia Gordon ▴ 480
0
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1
reply
1.3k
views
geneplotter - buildChromLoc for arrays with no .db package
GO geneplotter GO geneplotter
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ▴ 480
0
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13
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2.8k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 30
0
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1
reply
1.5k
views
Error installing geneplotter
geneplotter geneplotter
updated 13.3 years ago by ★ 8.2k • written 13.3 years ago by ★ 13k
0
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1
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1.5k
views
bug info
Microarray Normalization geneplotter graph limma Microarray Normalization geneplotter
updated 13.7 years ago by 6.7k • written 13.7 years ago by ▴ 10
0
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3
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2.2k
views
Bioconductor / plotting SNPs, runs of homozygosity
SNP geneplotter SNPchip SNP geneplotter SNPchip
updated 14.6 years ago by 6.7k • written 14.6 years ago by ▴ 40
0
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0
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2.5k
views
How to plot gene on their chromosome?
Annotation Cancer geneplotter idiogram rtracklayer Annotation Cancer geneplotter idiogram
15.8 years ago Martin Morgan 25k
0
votes
5
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1.9k
views
annotate incompatible with RdbiPgSQL !?!
annotate geneplotter Rdbi RdbiPgSQL annotate geneplotter Rdbi RdbiPgSQL
updated 15.8 years ago by 68k • written 15.8 years ago by ▴ 160
0
votes
0
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1.1k
views
Visulising KEGG pathways using KEGGSOAP - example code
Pathways geneplotter KEGGSOAP biomaRt GEOquery Pathways geneplotter KEGGSOAP biomaRt
15.9 years ago michael watson IAH-C ★ 3.4k
0
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5
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3.5k
views
From eSet to AffyBatch Object
geneplotter affy geneplotter affy
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 120
0
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3
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1.5k
views
Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
probe annotate geneplotter affy vsn Ringo probe annotate geneplotter affy vsn Ringo
updated 16.7 years ago by ▴ 730 • written 16.7 years ago by ▴ 110
0
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0
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1.1k
views
Colors in cColor from geneplotter
probe geneplotter probe geneplotter
16.7 years ago Heidi Dvinge ★ 2.0k
0
votes
0
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872
views
buildChromLocation with Drosophila2 Affy arrays
geneplotter geneplotter
16.9 years ago Blanchette, Marco ▴ 10
0
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2
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1.4k
views
Rgraphviz edge attributes can't be changed on Mac
Biobase geneplotter Rgraphviz Biobase geneplotter Rgraphviz
updated 17.3 years ago by ▴ 540 • written 17.3 years ago by ★ 1.6k
0
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4
replies
2.5k
views
Installing beadarray
annotate geneplotter beadarray AnnotationDbi annotate geneplotter beadarray AnnotationDbi
updated 17.3 years ago by 21k • written 17.3 years ago by ▴ 270
0
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1
reply
1.2k
views
Rgraphviz edge attributes can't be changed on Mac
geneplotter Rgraphviz geneplotter Rgraphviz
updated 17.3 years ago by 16k • written 17.3 years ago by ★ 1.6k
0
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1
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1.5k
views
Problem reading data with beadarray package
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 17.3 years ago by ▴ 460 • written 17.3 years ago by ▴ 10
0
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2
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1.3k
views
vsm2
Survival geneplotter affy vsn limma affyio Survival geneplotter affy vsn limma affyio
updated 17.4 years ago by ★ 13k • written 17.4 years ago by ▴ 70
0
votes
1
reply
1.3k
views
beadarray: combining several beadsummary data objects
Biobase geneplotter affy affyio beadarray Biobase geneplotter affy affyio beadarray
updated 17.4 years ago by ▴ 460 • written 17.4 years ago by ▴ 70
0
votes
4
replies
2.4k
views
disagreement between biomaRt and topGO
GO hgu133plus2 annotate geneplotter graph Rgraphviz PROcess goTools biomaRt Category GO
updated 17.5 years ago by ▴ 500 • written 17.5 years ago by ★ 1.4k
0
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6
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3.7k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
updated 17.5 years ago by ▴ 220 • written 17.5 years ago by ★ 2.2k
0
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0
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2.0k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
17.5 years ago Min Wook Kim ▴ 20
0
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2
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1.3k
views
AnnBuilder questions
Annotation GO Yeast hgu95av2 probe geneplotter AnnBuilder Annotation GO Yeast hgu95av2
updated 17.5 years ago by ★ 7.2k • written 17.5 years ago by ▴ 30
0
votes
1
reply
1.4k
views
beadarray - combing
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 17.6 years ago by ▴ 320 • written 17.6 years ago by ▴ 270
0
votes
1
reply
1.6k
views
ControlID Qcinfo slot in Illumina beadarray summary data?
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 17.6 years ago by ▴ 320 • written 17.6 years ago by ▴ 410
0
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3
replies
1.8k
views
beadarray package: problem with bead level data
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 17.6 years ago by ▴ 40 • written 17.6 years ago by ▴ 270
0
votes
1
reply
1.5k
views
snapCGH; export results of summarize.clones() function from aCGH
aCGH Survival Cancer Breast Biobase annotate genefilter geneplotter multtest limma aCGH
17.7 years ago Steven McKinney ▴ 310
0
votes
1
reply
1.3k
views
beadarray readIllumina suggestions
Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy
updated 17.7 years ago by ▴ 460 • written 17.7 years ago by ▴ 10
0
votes
3
replies
1.4k
views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ▴ 160
0
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4
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2.5k
views
smoothScatter axis limits
annotate geneplotter annotate geneplotter
updated 17.7 years ago by ★ 1.9k • written 17.7 years ago by ▴ 250
0
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0
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1.3k
views
RBGL: bfs & dfs with directed graphs
GO Biobase annotate geneplotter graph Rgraphviz annaffy RBGL convert GO Biobase graph
17.9 years ago stephen edwards ▴ 10
0
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2
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1.9k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.9 years ago by 52k • written 17.9 years ago by ▴ 680
0
votes
1
reply
1.5k
views
question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 17.9 years ago by 68k • written 17.9 years ago by ★ 2.2k
0
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0
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1.8k
views
Options for spatial normalization? (Oliver Homann)
SNP Microarray Annotation Normalization GO Classification Cancer annotate geneplotter SNP
18.0 years ago Tarca, Adi ▴ 570
0
votes
1
reply
973
views
Normalization in davidTiling demo
Normalization GO Survival Biobase genefilter geneplotter affy vsn PROcess tilingArray GO
updated 18.0 years ago by ★ 13k • written 18.0 years ago by ★ 1.3k
0
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1
reply
1.1k
views
Normalization in davidTiling demo
Normalization GO Survival genefilter geneplotter affy vsn tilingArray affyio GO Survival
updated 18.0 years ago by ★ 13k • written 18.0 years ago by ★ 1.3k
0
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4
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2.0k
views
[R-SIG-Mac] Mac os x graphviz-Rgraphviz problem
Biobase annotate geneplotter graph Rgraphviz BUS Biobase annotate geneplotter graph BUS
updated 18.1 years ago by ★ 7.4k • written 18.1 years ago by ★ 6.5k
0
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10
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2.3k
views
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
0
votes
12
replies
2.3k
views
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
0
votes
0
replies
1.5k
views
Re: Defining your own chromosome annotations
Microarray geneplotter limma AnnBuilder genomes Microarray geneplotter limma AnnBuilder
19.8 years ago Palmer, Lance ▴ 30
0
votes
1
reply
1.1k
views
Defining your own chromosome annotations
geneplotter genomes geneplotter genomes
updated 19.8 years ago by 21k • written 19.8 years ago by ▴ 30
0
votes
0
replies
1.2k
views
Detecting overrepresented genomic loci
aCGH Clustering CGH geneplotter DNAcopy aCGH GLAD aCGH Clustering CGH geneplotter aCGH
19.9 years ago Yi, Andrew ▴ 20
0
votes
2
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1.5k
views
Geneplotter, alongChrom problem
Organism geneplotter Organism geneplotter
updated 19.9 years ago by ★ 13k • written 19.9 years ago by ▴ 540
0
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2
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1.1k
views
greenred.colors() in geneplotter
geneplotter geneplotter
20.0 years ago michael watson IAH-C ★ 3.4k
0
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0
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963
views
Affy: chromosomal localization with expression value for of gene lists
Cancer geneplotter Cancer geneplotter
20.1 years ago John Zhang ★ 2.9k
0
votes
2
replies
1.9k
views
Installation Problem on OS X
GO geneplotter graph Rgraphviz pamr globaltest GO geneplotter graph Rgraphviz pamr
updated 20.3 years ago by ▴ 680 • written 20.3 years ago by ▴ 10
0
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2
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1.5k
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 20.3 years ago by ★ 7.4k • written 20.3 years ago by ▴ 130
50 results • Page 1 of 1
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Answer: WGCNA with paired samples by Ivo • 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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