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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
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
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
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 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
bernsmq
• 0
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
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
4.4k
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
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
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
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
13 results • Page
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Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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