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Goana
•
reset
15
votes
18
replies
3.4k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Raito92
▴ 60
13
votes
6
replies
6.2k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma
goana
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
carl.mann
▴ 20
6
votes
10
replies
5.2k
views
goana and "No annotated genes found in universe" even with Entrez gene ids
goana
edger
updated 2.3 years ago by
Gordon Smyth
50k • written 4.8 years ago by
matrs
▴ 10
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
Raito92
▴ 60
4
votes
3
replies
1.3k
views
including information indicating upregulation/downregulation of genes in goana()
edger
goana
updated 7.7 years ago by
James W. MacDonald
65k • written 7.7 years ago by
jhj89
▴ 10
3
votes
6
replies
2.3k
views
Strange output from goana()
edger
goana
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
cronanz
• 0
3
votes
2
replies
4.6k
views
No genes found in universe : goana error
edger
goana
gene ontology
6.6 years ago • updated 6.5 years ago
fawazfebin
▴ 60
3
votes
4
replies
1.3k
views
Cannot retrieve DE genes from goana GO terms
limma
goana
edger
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
b.nota
▴ 360
1
vote
2
replies
962
views
Results Goana after edgeR pipeline
EdgeR
Bioinformatics
Goana
2.7 years ago
Barista
• 0
0
votes
3
replies
421
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip
limma
goana
updated 5 months ago by
SamGG
▴ 350 • written 5 months ago by
samagbeyimodupe
• 0
0
votes
4
replies
1.9k
views
need help with microarray GO enrichment using goana
goana
limma
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
mat149
▴ 70
0
votes
2
replies
1.4k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 6.8 years ago by
Gordon Smyth
50k • written 7.0 years ago by
Jenny Drnevich
★ 2.0k
0
votes
4
replies
3.1k
views
No annotated genes found in universe error using goana and kegga
limma
goana
gene set enrichment
6.5 years ago
emy_66
• 0
0
votes
3
replies
2.5k
views
Using kegga and goana for Plants
edger
goana
kegga
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
jfreixas
• 0
0
votes
3
replies
1.2k
views
UnProducible error with goana and kegga function
limma
goana
kegga
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
Ahdee
▴ 50
0
votes
0
replies
3.0k
views
Create a Gene Enrichment GO plot from goana output
goana
RNASeq
edgeR
RnaSeq
GO
2.1 years ago
Raito92
▴ 60
16 results • Page
1 of 1
Recent ...
Replies
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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