Showing : Gostats • reset
0
votes
2
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716
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
6 weeks ago • updated 5 weeks ago GV Yoshikawa • 0
0
votes
0
replies
533
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
17 months ago georgii.vdovin • 0
0
votes
0
replies
586
views
plotGOTermGraph connects all subtrees to the root node
GO.db GOstats
18 months ago RuBBiT0 ▴ 10
1
vote
9
replies
1.6k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 21 months ago by • 0 • written 21 months ago by ▴ 380
2
votes
3
replies
2.1k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 20
1
vote
2
replies
1.1k
views
Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
3.8 years ago MOHAMMAD • 0
0
votes
0
replies
916
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.1 years ago Madza Farias-Virgens • 0
0
votes
1
reply
969
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 10
3
votes
4
replies
1.6k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
5.6 years ago Matthew Thornton ▴ 380
0
votes
5
replies
1.7k
views
hyperGTest not working on custom annotation package
GOstats AnnotationDbi GO.db
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
2
votes
2
replies
1.6k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
votes
2
replies
1.3k
views
comparing two GOstats result lists
gostats statistics
updated 6.5 years ago by 67k • written 6.5 years ago by ▴ 30
3
votes
10
replies
1.5k
views
GO Stats results contain GO terms NOT present in the gene universe
gostats
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 30
0
votes
1
reply
2.0k
views
how to run GO enrichment analysis for non-model organisms (errors when using hyperGTest)
gostats GO non_model
6.7 years ago zhaoran1124 • 0
0
votes
0
replies
1.4k
views
GOstats install Error : .onLoad failed in loadNamespace() for 'GO.db'
gostats go.db
6.8 years ago crafy • 0
0
votes
0
replies
1.4k
views
invalid names for slots of class GOHyperGResult
gostats
7.1 years ago laianavarromartin ▴ 20
0
votes
6
replies
1.9k
views
GO-terms delivered by GOstats hyperGTest() do not exist in my universe
GOstats
7.1 years ago martis.mihaela • 0
0
votes
1
reply
1.4k
views
Add gene information to most expressed gene list (packages lumi and GOstats)
annotation lumi GOstats
updated 7.2 years ago by 67k • written 7.2 years ago by • 0
0
votes
0
replies
1.1k
views
Question: Enrichment heatmap - GOstats package of R
Gostats p-value
7.4 years ago salamandra ▴ 20
0
votes
1
reply
1.1k
views
GOstats R Package
gostats
7.4 years ago arpa530 • 0
0
votes
0
replies
1.4k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.8 years ago avinash gupta ▴ 130
4
votes
2
replies
1.7k
views
Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
gostats hypergeometric test
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 10
6
votes
6
replies
3.8k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats go term annotation drosophila melanogaster error
updated 7.8 years ago by ▴ 10 • written 8.5 years ago by ▴ 300
2
votes
9
replies
4.3k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 760
1
vote
2
replies
1.6k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 8.4 years ago by 67k • written 8.4 years ago by • 0
2
votes
1
reply
1.3k
views
Is possible to use an organism annotation package in simLL function?
gostats
updated 8.4 years ago by 67k • written 8.4 years ago by ▴ 760
0
votes
4
replies
1.7k
views
Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools annotationhub gostats
updated 8.5 years ago by 67k • written 8.5 years ago by ▴ 20
0
votes
1
reply
3.8k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor r gostats
updated 8.5 years ago by 67k • written 8.5 years ago by • 0
0
votes
2
replies
1.4k
views
broken link to www.godatabase.org in results generated by htmlReport() from GOstats package ?
GOstats www.godatabase.org htmlReport
8.5 years ago c.kohler • 0
0
votes
3
replies
2.1k
views
Can not install 'affyio' with compiler icc on redhat linux ES5
GOstats GOstats
updated 8.5 years ago by ▴ 10 • written 14.1 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Problem with GOstats - invalid names for slots of class GOHyperGResult
GOstat GOstats
8.5 years ago ccanchaya • 0
0
votes
2
replies
3.1k
views
Odd Odds Ratio in GOstats package
GO GOstats GO GOstats
updated 8.7 years ago by • 0 • written 10.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Annotation, Over representation testing and Pathway analysis using Ensembl gene IDs
rnaseq annotation gostats org.Bt.eg.db
8.7 years ago mrodrigues.fernanda ▴ 10
13
votes
2
replies
4.9k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 9.1 years ago by ★ 3.4k • written 9.1 years ago by ▴ 40
1
vote
0
replies
1.5k
views
enrichment analysis for gene pairs
go gostats category gsea
9.2 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.5k
views
GoStats Hit Counter for website
gostats gostat
updated 9.2 years ago by ★ 8.2k • written 9.2 years ago by • 0
0
votes
1
reply
1.6k
views
GOstats and termGraph - Getting all of the plots out of the list
gostats rgraphviz
updated 9.3 years ago by ★ 6.8k • written 9.4 years ago by • 0
0
votes
0
replies
1.5k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
9.4 years ago petyuk ▴ 70
0
votes
2
replies
1.3k
views
Conditional test for goseq?
goseq gostats
updated 9.4 years ago by 52k • written 9.4 years ago by ★ 2.1k
0
votes
8
replies
2.4k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 9.6 years ago by ★ 1.2k • written 9.6 years ago by ▴ 930
1
vote
2
replies
1.5k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings gostats
updated 9.7 years ago by 67k • written 9.7 years ago by • 0
0
votes
1
reply
1.1k
views
Alien GO result from GOstats
gostats
9.7 years ago Yue Zhao • 0
0
votes
3
replies
1.8k
views
Genes corresponding to GO terms for unsupported organsims
gostats unsupported organisms
updated 9.8 years ago by ★ 7.2k • written 9.8 years ago by ▴ 270
1
vote
10
replies
2.6k
views
Filtering genes for GOstats
gostats
9.9 years ago • updated 9.8 years ago nonCodingGene ▴ 10
0
votes
1
reply
1.9k
views
Customized GO enrichment with GOstat
GOstats
updated 9.9 years ago by 67k • written 9.9 years ago by • 0
0
votes
6
replies
2.4k
views
hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term
Annotation GO gostats
updated 10.0 years ago by 52k • written 12.1 years ago by ▴ 70
0
votes
2
replies
2.0k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 10.1 years ago by 67k • written 10.1 years ago by • 0
3
votes
3
replies
2.6k
views
GOstats "count" question
gostats
updated 10.1 years ago by 67k • written 10.2 years ago by ▴ 10
4
votes
3
replies
3.3k
views
Select the annotation level during GO enrichment
topgo gostats go
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 80
0
votes
0
replies
2.5k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.3 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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