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kegga
•
reset
2
votes
15
replies
3.9k
views
Timeout error in kegga() using edgeR
edger
kegga
keggrest
8.3 years ago
Likai Mao
▴ 40
7
votes
11
replies
6.4k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR
limma
annotationhub
kegga
annotationdbi
updated 7.8 years ago by
cagenet34
▴ 20 • written 8.1 years ago by
Rinaldo Bertossa
▴ 20
8
votes
8
replies
4.8k
views
how to use "non-standard" species for KEGG / GO analysis in limma?
limma
kegga
goanna
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Guido Hooiveld
★ 3.9k
3
votes
6
replies
1.9k
views
How to create a customized OrgDb in order to perform kegga analysis?
limma
kegga
orgdb
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
baus87
• 0
0
votes
5
replies
2.6k
views
How to use topGO and KEGG with de-novo species
topgo
edger
limma
kegga
kegg
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
mictadlo
▴ 10
0
votes
5
replies
4.4k
views
How to select the genes mapped to an enriched KEGG pathway (kegga)
kegga
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
mat149
▴ 70
5
votes
4
replies
1.6k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga
limma
pathway analysis
kegg
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Raito92
▴ 60
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
1
vote
3
replies
1.7k
views
KEGG pathway analysis on a predefined set of genes (with my own annotation)?
limma
kegga
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
miyakokodama
• 0
0
votes
3
replies
1.4k
views
kegga() p-value calculated differently in different edgeR versions
edger
kegga
updated 6.9 years ago by
Gordon Smyth
50k • written 6.9 years ago by
cronanz
• 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
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
1
reply
1.0k
views
Is there a way to specify the pathway level of classification that we want in kegga function from edgeR?
edgeR
kegga
KEGG
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
bernsmq
• 0
13 results • Page
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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