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kegga
•
reset
2
votes
15
replies
3.8k
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
0
votes
3
replies
1.4k
views
kegga() p-value calculated differently in different edgeR versions
edger
kegga
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
cronanz
• 0
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
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
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
1
reply
1000
views
Is there a way to specify the pathway level of classification that we want in kegga function from edgeR?
edgeR
kegga
KEGG
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
bernsmq
• 0
8
votes
8
replies
4.7k
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
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
5
replies
4.3k
views
How to select the genes mapped to an enriched KEGG pathway (kegga)
kegga
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 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 6.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
5
replies
2.6k
views
How to use topGO and KEGG with de-novo species
topgo
edger
limma
kegga
kegg
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
mictadlo
▴ 10
0
votes
3
replies
2.4k
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
13 results • Page
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Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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