Showing : geneplotter • reset
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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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5
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1.0k
views
getBioC v1.2.22 & [R] v1.6.2
annotate edd genefilter geneplotter rhdf5 multtest ROC tkWidgets reposTools affy vsn
updated 19.2 years ago by ★ 3.9k • written 19.2 years ago by ▴ 70
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3
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contributing to Bioconductor
GO Clustering geneplotter GO Clustering geneplotter
19.2 years ago Wilkinson, Mark ▴ 60
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5
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653
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Recent changes to Bioconductor packages
SAGE annotate geneplotter graph SAGElyzer Rdbi SAGE annotate geneplotter graph SAGElyzer
19.3 years ago madman@jimmy.harvard.edu ▴ 850
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3
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1.1k
views
beadarray package: problem with bead level data
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.8 years ago by ▴ 40 • written 14.8 years ago by ▴ 270
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4
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1.1k
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[R-SIG-Mac] Mac os x graphviz-Rgraphviz problem
Biobase annotate geneplotter graph Rgraphviz BUS Biobase annotate geneplotter graph BUS
updated 15.3 years ago by ★ 7.4k • written 15.3 years ago by 6.5k
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2
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vsm2
Survival geneplotter affy vsn limma affyio Survival geneplotter affy vsn limma affyio
updated 14.7 years ago by 13k • written 14.7 years ago by ▴ 70
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2
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views
AnnBuilder questions
Annotation GO Yeast hgu95av2 probe geneplotter AnnBuilder Annotation GO Yeast hgu95av2
updated 14.8 years ago by ★ 7.2k • written 14.8 years ago by ▴ 30
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4
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disagreement between biomaRt and topGO
GO hgu133plus2 annotate geneplotter graph Rgraphviz PROcess goTools biomaRt Category GO
updated 14.7 years ago by ▴ 500 • written 14.7 years ago by ★ 1.4k
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2
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views
Rgraphviz edge attributes can't be changed on Mac
Biobase geneplotter Rgraphviz Biobase geneplotter Rgraphviz
updated 14.6 years ago by ▴ 540 • written 14.6 years ago by ★ 1.5k
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2
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928
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 17.6 years ago by ★ 7.4k • written 17.6 years ago by ▴ 130
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2
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views
Installation Problem on OS X
GO geneplotter graph Rgraphviz pamr globaltest GO geneplotter graph Rgraphviz pamr
updated 17.5 years ago by ▴ 680 • written 17.5 years ago by ▴ 10
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2
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526
views
greenred.colors() in geneplotter
geneplotter geneplotter
17.3 years ago michael watson IAH-C ★ 3.4k
0
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12
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1.1k
views
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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2
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1.1k
views
"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 15.2 years ago by ▴ 680
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4
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1.6k
views
smoothScatter axis limits
annotate geneplotter annotate geneplotter
updated 15.0 years ago by ★ 1.9k • written 15.0 years ago by ▴ 250
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3
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views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 15.0 years ago by ★ 7.4k • written 15.0 years ago by ▴ 160
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6
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2.4k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
updated 14.8 years ago by ▴ 220 • written 14.8 years ago by ★ 2.2k
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4
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1.7k
views
Installing beadarray
annotate geneplotter beadarray AnnotationDbi annotate geneplotter beadarray AnnotationDbi
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 270
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5
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2.6k
views
From eSet to AffyBatch Object
geneplotter affy geneplotter affy
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 120
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5
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1.2k
views
annotate incompatible with RdbiPgSQL !?!
annotate geneplotter Rdbi RdbiPgSQL annotate geneplotter Rdbi RdbiPgSQL
updated 13.1 years ago by 59k • written 13.1 years ago by ▴ 160
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1
reply
527
views
Help using annotation data without explicitly building data package
Annotation geneplotter Annotation geneplotter
updated 18.6 years ago by 6.6k • written 18.6 years ago by 21k
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1
reply
503
views
Normalization in davidTiling demo
Normalization GO Survival Biobase genefilter geneplotter affy vsn PROcess tilingArray GO
updated 15.2 years ago by 13k • written 15.2 years ago by ★ 1.3k
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1
reply
951
views
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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3
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1.4k
views
Bioconductor / plotting SNPs, runs of homozygosity
SNP geneplotter SNPchip SNP geneplotter SNPchip
updated 11.9 years ago by 6.6k • written 11.9 years ago by ▴ 40
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1
reply
981
views
Error installing geneplotter
geneplotter geneplotter
updated 10.6 years ago by ★ 8.2k • written 10.6 years ago by ★ 12k
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13
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1.6k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 30
0
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1
reply
828
views
beadarray readIllumina suggestions
Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy
updated 14.9 years ago by ▴ 460 • written 14.9 years ago by ▴ 10
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1
reply
839
views
snapCGH; export results of summarize.clones() function from aCGH
aCGH Survival Cancer Breast Biobase annotate genefilter geneplotter multtest limma aCGH
14.9 years ago Steven McKinney ▴ 310
0
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1
reply
846
views
ControlID Qcinfo slot in Illumina beadarray summary data?
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.8 years ago by ▴ 320 • written 14.8 years ago by ▴ 410
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1
reply
824
views
beadarray - combing
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.8 years ago by ▴ 320 • written 14.8 years ago by ▴ 270
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1
reply
756
views
geneplotter - buildChromLoc for arrays with no .db package
GO geneplotter GO geneplotter
updated 9.5 years ago by ★ 7.2k • written 9.5 years ago by ▴ 480
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1
reply
750
views
beadarray: combining several beadsummary data objects
Biobase geneplotter affy affyio beadarray Biobase geneplotter affy affyio beadarray
updated 14.7 years ago by ▴ 460 • written 14.7 years ago by ▴ 70
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1
reply
705
views
Errors w/ getBioC(develOK =TRUE) with R2.0 devel
aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy
17.7 years ago Matthew Hannah ▴ 940
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1
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967
views
Problem reading data with beadarray package
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.6 years ago by ▴ 460 • written 14.6 years ago by ▴ 10
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1
reply
790
views
Rgraphviz edge attributes can't be changed on Mac
geneplotter Rgraphviz geneplotter Rgraphviz
updated 14.6 years ago by 15k • written 14.6 years ago by ★ 1.5k
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3
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812
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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 13.9 years ago by ▴ 720 • written 13.9 years ago by ▴ 110
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1
reply
1.2k
views
Problems with url/download and http_proxy
Biobase annotate edd geneplotter tkWidgets ASSIGN Biobase annotate edd geneplotter
updated 19.9 years ago by ▴ 50 • written 19.9 years ago by ▴ 460
6
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5
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views
Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
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1
reply
940
views
bug info
Microarray Normalization geneplotter graph limma Microarray Normalization geneplotter
updated 11.0 years ago by 6.6k • written 11.0 years ago by ▴ 10
0
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1
reply
545
views
[bioC] GenePlotter for mgu74v2
GO Cancer mgu74a mgu74av2 geneplotter GO Cancer mgu74a mgu74av2 geneplotter
updated 19.1 years ago by ★ 5.5k • written 19.1 years ago by ★ 2.9k
0
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1
reply
593
views
using geneplotter with my own data
geneplotter geneplotter
updated 19.0 years ago by ★ 3.9k • written 19.0 years ago by ▴ 80
0
votes
1
reply
745
views
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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votes
1
reply
603
views
Plotting together data from hgu133a and b
hgu133a hgu133b geneplotter hgu133a hgu133b geneplotter
updated 17.8 years ago by ★ 5.5k • written 17.8 years ago by ▴ 500
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1
reply
1.4k
views
install geneplotter
geneplotter geneplotter
updated 8.4 years ago by 59k • written 8.4 years ago by ★ 12k
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2
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878
views
Geneplotter, alongChrom problem
Organism geneplotter Organism geneplotter
updated 17.2 years ago by 13k • written 17.2 years ago by ▴ 540
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1
reply
491
views
Defining your own chromosome annotations
geneplotter genomes geneplotter genomes
updated 17.1 years ago by 21k • written 17.1 years ago by ▴ 30
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votes
1
reply
627
views
Normalization in davidTiling demo
Normalization GO Survival genefilter geneplotter affy vsn tilingArray affyio GO Survival
updated 15.2 years ago by 13k • written 15.2 years ago by ★ 1.3k
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0
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525
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geneplotter and base position
Annotation geneplotter affy Annotation geneplotter affy
18.0 years ago david neil hayes ▴ 70
0
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1.0k
views
peer review process/DATE CORRECTION
Biobase annotate edd genefilter geneplotter rhdf5 multtest ROC tkWidgets affy AnnBuilder
20.1 years ago Vincent J. Carey, Jr. 6.6k
50 results • Page 1 of 1
Recent ...
Replies
Answer: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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