Showing : TOPGO • reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.4 years ago by ★ 3.3k • written 8.4 years ago by ▴ 40
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by ▴ 10
5
votes
7
replies
1.1k
views
Unexpected error with topGO, cannot build topGOdata object
topGO
4.0 years ago abf ▴ 30
5
votes
2
replies
1.9k
views
What is Nontrivial node in topGO analysis?
topgo
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
5
votes
1
reply
1.3k
views
topGO under-representation table
topGO GO
7.2 years ago • updated 7.1 years ago beachboarder900 ▴ 40
4
votes
7
replies
1.9k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by • 0
4
votes
3
replies
2.2k
views
topGO error "No function to select the significant genes provided!"
topgo
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 40
4
votes
4
replies
1.3k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 3.6 years ago by 50k • written 3.6 years ago by ▴ 120
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 14 months ago by 65k • written 3.9 years ago by ▴ 30
4
votes
3
replies
3.9k
views
topGO: significant genes in GO enriched categories
topGO
updated 9.0 years ago by ▴ 30 • written 9.1 years ago by ▴ 140
4
votes
2
replies
2.6k
views
error with display of significant nodes using topGO
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 14.6 years ago by ▴ 400 • written 14.6 years ago by ▴ 340
4
votes
3
replies
2.8k
views
Select the annotation level during GO enrichment
topgo gostats go
updated 9.6 years ago by 65k • written 9.6 years ago by ▴ 80
4
votes
8
replies
5.8k
views
topGO error: allGenes should be a factor or a numeric vector
topGO topgo GO term analysis
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by ▴ 10
3
votes
3
replies
1.2k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
3
votes
4
replies
1.7k
views
Trying to account for gene length in topGO analysis
topgo goseq deseq2
updated 7.8 years ago by ▴ 610 • written 7.8 years ago by • 0
3
votes
3
replies
1.0k
views
DEXUSResult as.data.frame doesn't work well if topGO is loaded
dexus topgo
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
3
votes
0
replies
1.7k
views
Interpret topGO reults
topGO reults
8.8 years ago megerdes ▴ 40
3
votes
2
replies
2.3k
views
How to use TopGO with gene symbols extracted from Illumina probes
topgo
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 50
3
votes
4
replies
1.6k
views
Different geneset same p-values in topGO
topgo bug
7.3 years ago • updated 3.6 years ago Lluís Revilla Sancho ▴ 730
3
votes
9
replies
4.7k
views
topGO "invalid argument to unary operator"
software error topgo
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
2
votes
6
replies
1.9k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
2
votes
2
replies
2.1k
views
topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 60
2
votes
2
replies
3.6k
views
topGO and font size in the graph plots
topGO topGO
updated 6.3 years ago by ▴ 20 • written 15.6 years ago by ▴ 10
2
votes
1
reply
1.1k
views
TopGO 0 nontrivial nodes
topGO topGO
10.8 years ago Dario Strbenac ★ 1.5k
2
votes
4
replies
2.1k
views
topGO crashes with ' argument "annotationFun" is missing, with no default'
bug topGO
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 160
2
votes
1
reply
2.2k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 6.8 years ago by ▴ 10 • written 8.1 years ago by ▴ 20
2
votes
1
reply
1.2k
views
TopGO - Incorrect mapping genes to GO terms
topgo go org.mm.eg.db
updated 6.2 years ago by 65k • written 6.2 years ago by • 0
2
votes
2
replies
4.3k
views
topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 7.0 years ago by ▴ 730 • written 7.0 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Error in topGO analysis
software error topGO go
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
2
votes
1
reply
1.9k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 3.3 years ago by ▴ 20 • written 11.1 years ago by ▴ 340
2
votes
0
replies
925
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
2
votes
4
replies
1.3k
views
topGO: how to rettrieve (long) GO term description without abbreviating
topGO
5.8 years ago al-ash ▴ 50
1
vote
1
reply
1.1k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 10
1
vote
6
replies
1.4k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
1
vote
1
reply
1.1k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.3 years ago David ROUX ▴ 20
1
vote
1
reply
908
views
topGO enrichment analysis
topgo
5.8 years ago prakashpandey1111 • 0
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.1 years ago digrigor ▴ 10
1
vote
3
replies
1.3k
views
topGo custom Annotation table
customannotation enrichmentanalysis topGO
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
vote
2
replies
1.4k
views
Error when using the showGroupDensity function in topGO
topGO
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 30
1
vote
2
replies
2.5k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 7.3 years ago by ▴ 730 • written 7.6 years ago by ▴ 10
1
vote
1
reply
1.7k
views
Pathview & topGO
R GO topGO pathview
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 10
1
vote
4
replies
1.6k
views
Obsolete GO terms in topGO analysis
topgo
8.5 years ago s.apocarpum ▴ 10
1
vote
3
replies
1.5k
views
TopGO significant genes
TopGO GO
4.0 years ago Al-a ▴ 10
1
vote
1
reply
1.9k
views
topGO - genesInTerm returns genes not in the annotation
topGO
9.1 years ago samuel collombet ▴ 140
1
vote
1
reply
5.2k
views
Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 150
1
vote
4
replies
4.1k
views
[topGO] More flexible way to select 'interesting' genes
GO probe topGO GO probe topGO
updated 10.7 years ago by ▴ 400 • written 10.7 years ago by ▴ 660
1
vote
0
replies
952
views
New GO terms after TopGO enrichment? (updated)
GO topGO GO topGO
10.5 years ago biotech ▴ 160
1
vote
0
replies
2.1k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
12.2 years ago Paul Geeleher ★ 1.3k
1
vote
0
replies
987
views
GO graphs made with topGO are unreadable
GO graph topGO GO graph topGO
11.3 years ago Guest User ★ 13k
1
vote
2
replies
1.2k
views
Absence of GO terms for some genes of interest in topGO package
topgo
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
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biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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