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goexpress
•
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9
votes
8
replies
5.6k
views
heatmap of genes based on enriched GO categories
goexpress
gopro
8.9 years ago
Bogdan
▴ 670
6
votes
7
replies
4.8k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
10.3 years ago
martin.hoelzer
▴ 20
5
votes
4
replies
2.2k
views
Contrasts in GOexpress analysis?
gene ontology
goexpress
updated 9.0 years ago by
kevin.rue
▴ 350 • written 9.0 years ago by
mforde84
▴ 20
3
votes
2
replies
1.8k
views
Is it common to get all 0 values when running the randomForest step in GOexpress?
goexpress
updated 10.2 years ago by
kevin.rue
▴ 350 • written 10.2 years ago by
willj
▴ 30
3
votes
6
replies
2.4k
views
GOexpress error at pValue_GO step
software error
goexpress
updated 10.2 years ago by
kevin.rue
▴ 350 • written 10.2 years ago by
kcamnairb
▴ 10
2
votes
8
replies
2.1k
views
Errors when plotting data using heatmap_GO (GOexpress)
GOexpress
updated 3.2 years ago by
kevin.rue
▴ 350 • written 3.2 years ago by
grolo
• 0
2
votes
6
replies
3.3k
views
GOexpress: GO_analyse function throws Error: Space required after the Public Identifier
goexpress
updated 9.9 years ago by
kevin.rue
▴ 350 • written 9.9 years ago by
martin.hoelzer
▴ 20
2
votes
4
replies
1.9k
views
GOexpress - Trouble with subset_scores result (<0 rows>)
GOexpress
subset_scores
<0 rows>
8.0 years ago
sina.zboron
• 0
1
vote
2
replies
2.0k
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress
heatmap
gene ontology
plot
updated 6.3 years ago by
kevin.rue
▴ 350 • written 6.3 years ago by
Antonio Campos
• 0
0
votes
2
replies
1.5k
views
'GO_analyse' function error
goexpress
ExpressionSet
GO_analyse
6.4 years ago
rezashiralmohammad
• 0
0
votes
4
replies
1.7k
views
GOexpress - Error when plotting expression data
RNA-seq
transcriptomics
gene ontology
gene expression
GOexpress
updated 6.0 years ago by
kevin.rue
▴ 350 • written 6.0 years ago by
atorson
• 0
0
votes
2
replies
3.4k
views
Can't install GO.db
GOexpress
GO.db
GOSemSim
3.2 years ago
Chruut
• 0
0
votes
0
replies
739
views
GOexpress pvalue and gene sets
GOexpress
3.9 years ago
jms2520
▴ 10
0
votes
3
replies
4.7k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo
biomart
gene ontology
goexpress
pathway analysis
updated 9.7 years ago by
kevin.rue
▴ 350 • written 9.7 years ago by
Darya Vanichkina
▴ 130
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Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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