Showing : GOstats • reset
13
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2
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4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.4 years ago by ★ 3.2k • written 8.4 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 7.2 years ago by ▴ 10 • written 7.9 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
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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
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1.4k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
4.9 years ago Matthew Thornton ▴ 350
3
votes
3
replies
2.3k
views
GOstats "count" question
gostats
updated 9.5 years ago by 65k • written 9.5 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 5.9 years ago by • 0 • written 5.9 years ago by ▴ 20
2
votes
4
replies
1.2k
views
GOstats minus IEA?
GOstats GOstats
updated 14.0 years ago by 6.7k • written 14.0 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 7.7 years ago by 65k • written 7.7 years ago by ▴ 730
2
votes
9
replies
3.9k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 7.4 years ago by 25k • written 7.5 years ago by ▴ 730
2
votes
2
replies
1.3k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
2
votes
3
replies
1.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 2.4 years ago by 65k • written 2.4 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 13 months ago by • 0 • written 13 months ago by ▴ 350
1
vote
2
replies
889
views
Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
3.1 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 7.7 years ago by 65k • written 7.7 years ago by • 0
1
vote
10
replies
2.3k
views
Filtering genes for GOstats
gostats
9.2 years ago nonCodingGene ▴ 10
1
vote
1
reply
1.3k
views
GoStats Hit Counter for website
gostats gostat
updated 8.5 years ago by ★ 8.2k • written 8.5 years ago by • 0
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go gostats category gsea
8.5 years ago Hector Corrada Bravo ▴ 60
1
vote
2
replies
1.3k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings gostats
updated 9.0 years ago by 65k • written 9.0 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 19.8 years ago by ▴ 300
0
votes
1
reply
750
views
Error loading GOstats
GOstats GOstats
updated 19.9 years ago by ★ 3.9k • written 19.9 years ago by ▴ 620
0
votes
2
replies
1.0k
views
lumi, lumiHumanV2 and GOstats
GO lumiHumanV2 GOstats lumi GO lumiHumanV2 GOstats lumi
updated 15.9 years ago by 65k • written 15.9 years ago by ▴ 270
0
votes
0
replies
768
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 19.2 years ago by ★ 3.4k • written 19.2 years ago by ▴ 720
0
votes
2
replies
908
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 18.9 years ago by ★ 7.4k • written 18.9 years ago by ▴ 300
0
votes
6
replies
1.4k
views
Many missing GO terms from GOHyperG call using mgu74av2
GO Survival hgu95av2 mgu74av2 Ruuid annotate multtest affy graph annaffy RBGL GOstats
updated 18.8 years ago by ★ 7.4k • written 18.8 years ago by ★ 1.4k
0
votes
0
replies
596
views
were are the XML and xtable packages?
GOstats widgetInvoke GOstats widgetInvoke
18.8 years ago Seth Falcon ★ 7.4k
0
votes
1
reply
791
views
GOstats/tkWidgets/gcrma conflict
tkWidgets gcrma matchprobes GOstats tkWidgets gcrma matchprobes GOstats
updated 18.4 years ago by 25k • written 18.4 years ago by ▴ 80
0
votes
1
reply
884
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
3.5k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor r gostats
updated 7.8 years ago by 65k • written 7.8 years ago by • 0
0
votes
1
reply
1.2k
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
566
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 19.7 years ago by ★ 3.9k • written 19.7 years ago by ▴ 20
0
votes
2
replies
1.7k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 9.4 years ago by 65k • written 9.4 years ago by • 0
0
votes
1
reply
1.0k
views
GO package for GOstats
GO GOstats GO GOstats
updated 19.7 years ago by ★ 3.9k • written 19.7 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 17.7 years ago by ★ 7.4k • written 17.7 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 19.7 years ago by ★ 5.5k • written 19.7 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
984
views
GOstats and library ath1121501
ath1121501 hgu95av2 GOstats ath1121501 hgu95av2 GOstats
updated 17.6 years ago by ★ 7.4k • written 17.6 years ago by ▴ 70
0
votes
1
reply
715
views
about packages GO, Gostats,...
GO GOstats Category GO GOstats Category
updated 17.6 years ago by 65k • written 17.6 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
669
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
2.1k
views
GOstats and KEGG
Pathways GO GOstats Pathways GO GOstats
updated 17.4 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 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 890
0
votes
1
reply
941
views
GOENTREZID2GO hard-coded in GOstats:makeGOGraph
Annotation GO Network Yeast graph GOstats Annotation GO Network Yeast graph GOstats
updated 17.3 years ago by ★ 7.4k • written 17.3 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
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Thanks ATpoint for you advice. Just don't understand the math behind the change in raw p value in this case. I think it is important to und…
Answer: Why p value inconsistent when using different number of pathway score? by ATpoint ★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Votes
Answer: Why p value inconsistent when using different number of pathway score?
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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