Showing : gostats • reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.5 years ago by ★ 3.3k • written 8.5 years ago by ▴ 40
6
votes
6
replies
3.4k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats go term annotation drosophila melanogaster error
updated 7.3 years ago by ▴ 10 • written 8.0 years ago by ▴ 300
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
2
replies
1.5k
views
Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
gostats hypergeometric test
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 10
3
votes
4
replies
1.4k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
5.0 years ago Matthew Thornton ▴ 360
3
votes
3
replies
2.3k
views
GOstats "count" question
gostats
updated 9.6 years ago by 65k • written 9.6 years ago by ▴ 10
3
votes
10
replies
1.3k
views
GO Stats results contain GO terms NOT present in the gene universe
gostats
updated 6.0 years ago by • 0 • written 6.0 years ago by ▴ 20
2
votes
4
replies
1.2k
views
GOstats minus IEA?
GOstats GOstats
updated 14.1 years ago by 6.7k • written 14.1 years ago by ★ 1.0k
2
votes
1
reply
1.2k
views
Is possible to use an organism annotation package in simLL function?
gostats
updated 7.8 years ago by 65k • written 7.8 years ago by ▴ 730
2
votes
9
replies
4.0k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 730
2
votes
2
replies
1.4k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
2
votes
3
replies
1.7k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 20
1
vote
9
replies
1.2k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 14 months ago by • 0 • written 14 months ago by ▴ 360
1
vote
2
replies
912
views
Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
3.2 years ago MOHAMMAD • 0
1
vote
2
replies
1.4k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 7.8 years ago by 65k • written 7.8 years ago by • 0
1
vote
10
replies
2.3k
views
Filtering genes for GOstats
gostats
9.3 years ago • updated 9.2 years ago nonCodingGene ▴ 10
1
vote
1
reply
1.4k
views
GoStats Hit Counter for website
gostats gostat
updated 8.6 years ago by ★ 8.2k • written 8.6 years ago by • 0
1
vote
0
replies
1.4k
views
enrichment analysis for gene pairs
go gostats category gsea
8.6 years ago Hector Corrada Bravo ▴ 60
1
vote
2
replies
1.3k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings gostats
updated 9.1 years ago by 65k • written 9.1 years ago by • 0
0
votes
2
replies
1.1k
views
(no subject)
GO GOstats GO GOstats
updated 19.8 years ago by ▴ 10 • written 19.9 years ago by ▴ 300
0
votes
1
reply
762
views
Error loading GOstats
GOstats GOstats
updated 20.0 years ago by ★ 3.9k • written 20.0 years ago by ▴ 620
0
votes
2
replies
1.0k
views
lumi, lumiHumanV2 and GOstats
GO lumiHumanV2 GOstats lumi GO lumiHumanV2 GOstats lumi
updated 16.0 years ago by 65k • written 16.0 years ago by ▴ 270
0
votes
0
replies
792
views
error with the function GOHyperG from GOstats package
GO GOstats GO GOstats
19.0 years ago Sabrina Carpentier ▴ 70
0
votes
6
replies
1.2k
views
.pdf files of GOstats documents
GOstats GOstats
updated 19.3 years ago by ★ 3.4k • written 19.3 years ago by ▴ 720
0
votes
2
replies
918
views
GOstats
GOstats GOstats
updated 19.3 years ago by 21k • written 19.3 years ago by ▴ 100
0
votes
4
replies
1.3k
views
Error with Rgraphviz
GOstats GOstats
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ▴ 300
0
votes
6
replies
1.5k
views
Many missing GO terms from GOHyperG call using mgu74av2
GO Survival hgu95av2 mgu74av2 Ruuid annotate multtest affy graph annaffy RBGL GOstats
updated 18.9 years ago by ★ 7.4k • written 18.9 years ago by ★ 1.4k
0
votes
0
replies
602
views
were are the XML and xtable packages?
GOstats widgetInvoke GOstats widgetInvoke
18.9 years ago Seth Falcon ★ 7.4k
0
votes
1
reply
799
views
GOstats/tkWidgets/gcrma conflict
tkWidgets gcrma matchprobes GOstats tkWidgets gcrma matchprobes GOstats
updated 18.5 years ago by 25k • written 18.5 years ago by ▴ 80
0
votes
1
reply
901
views
rbind in annaffy problem
GO hgu95av2 rat2302 cdf annotate affy graph annaffy RBGL GOstats biomaRt GO hgu95av2
updated 18.4 years ago by 65k • written 18.4 years ago by ▴ 890
0
votes
1
reply
3.6k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor r gostats
updated 7.9 years ago by 65k • written 7.9 years ago by • 0
0
votes
1
reply
1.3k
views
hyperGTest Error in sqliteExecStatement...
GO hgu95av2 GOstats GO hgu95av2 GOstats
updated 16.0 years ago by ★ 5.5k • written 16.0 years ago by ▴ 10
0
votes
7
replies
1.3k
views
Odds Ratio in GOstat [resolved?]
GOstats Category GOstats Category
updated 17.4 years ago by ★ 6.0k • written 17.4 years ago by ★ 7.4k
0
votes
0
replies
578
views
Bug in function hasGOannote() form GOstats package
GOstats GOstats
19.5 years ago Adrian Alexa ▴ 400
0
votes
9
replies
1.4k
views
Rgraphviz for Windows
Rgraphviz GOstats Rgraphviz GOstats
updated 19.8 years ago by ★ 3.9k • written 19.8 years ago by ▴ 20
0
votes
2
replies
1.8k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 9.5 years ago by 65k • written 9.5 years ago by • 0
0
votes
1
reply
1.0k
views
GO package for GOstats
GO GOstats GO GOstats
updated 19.8 years ago by ★ 3.9k • written 19.8 years ago by ▴ 20
0
votes
3
replies
1.4k
views
hypergeometric enrichment of GO terms
Microarray GO GOstats biomaRt Microarray GO GOstats biomaRt
updated 17.7 years ago by ★ 13k • written 17.7 years ago by ▴ 30
0
votes
2
replies
1.0k
views
error with GOHyperG
drosophila2 cdf Biobase annotate genefilter multtest RBGL GOstats drosophila2 cdf RBGL
updated 17.8 years ago by ★ 7.4k • written 17.8 years ago by ▴ 10
0
votes
2
replies
1.1k
views
where can I find the GO and xtable package?
GO Biobase annotate genefilter graph RBGL GOstats GO Biobase annotate genefilter graph
updated 19.8 years ago by ★ 5.5k • written 19.8 years ago by ▴ 320
0
votes
1
reply
1.2k
views
GO annotation/analysis for ath1121501
Annotation GO ath1121501 goTools GOstats biomaRt Annotation GO ath1121501 goTools
updated 17.7 years ago by ▴ 870 • written 17.7 years ago by ▴ 340
0
votes
2
replies
999
views
GOstats and library ath1121501
ath1121501 hgu95av2 GOstats ath1121501 hgu95av2 GOstats
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ▴ 70
0
votes
1
reply
726
views
about packages GO, Gostats,...
GO GOstats Category GO GOstats Category
updated 17.7 years ago by 65k • written 17.7 years ago by ▴ 70
0
votes
3
replies
2.0k
views
Situation of the legend in the plotPCA of the affycoretools library
GO Survival cdf annotate genefilter multtest affy graph limma RBGL GOstats Category GO
updated 17.6 years ago by 65k • written 17.6 years ago by ▴ 350
0
votes
1
reply
675
views
reference question
AnnBuilder GOstats AnnBuilder GOstats
updated 17.6 years ago by ★ 13k • written 17.6 years ago by ▴ 310
0
votes
6
replies
2.2k
views
GOstats and KEGG
Pathways GO GOstats Pathways GO GOstats
updated 17.5 years ago by ★ 7.4k • written 17.5 years ago by ▴ 190
0
votes
0
replies
1.1k
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
17.5 years ago James W. MacDonald 65k
0
votes
5
replies
1.5k
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 17.5 years ago by ★ 7.4k • written 17.5 years ago by ▴ 890
0
votes
1
reply
958
views
GOENTREZID2GO hard-coded in GOstats:makeGOGraph
Annotation GO Network Yeast graph GOstats Annotation GO Network Yeast graph GOstats
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ★ 1.1k
0
votes
0
replies
1.3k
views
Error in makeOrgPackageFromNCBI
GO OrgDb annotate GOstats GO OrgDb annotate GOstats
10.9 years ago Chris Whelan ▴ 60
50 results • Page 1 of 1
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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