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missmethyl
•
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0
votes
0
replies
337
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
12 months ago
nurkenber
• 0
0
votes
1
reply
639
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
maximuscfyeung
• 0
0
votes
2
replies
707
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
maximuscfyeung
• 0
0
votes
2
replies
1.1k
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 16 months ago by
nrenke
• 0 • written 17 months ago by
Lucie
• 0
1
vote
3
replies
2.2k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
22 months ago • updated 15 months ago
s.malik
• 0
0
votes
1
reply
1.2k
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 2.4 years ago by
Tim Peters
▴ 230 • written 2.4 years ago by
b.curran
• 0
0
votes
2
replies
1.2k
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 21 months ago by
CHEN
• 0 • written 2.7 years ago by
Saanchi
• 0
1
vote
1
reply
1.1k
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 2.7 years ago by
belinda.phipson
▴ 40 • written 2.7 years ago by
Grace
• 0
0
votes
1
reply
1.0k
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
2.7 years ago
Grace
• 0
0
votes
0
replies
692
views
goMeth
missMethyl
2.8 years ago
anmolanp
▴ 10
2
votes
6
replies
1.8k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 2.8 years ago by
belinda.phipson
▴ 40 • written 2.8 years ago by
Joana
• 0
2
votes
3
replies
2.1k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 3.0 years ago by
belinda.phipson
▴ 40 • written 3.0 years ago by
Lukas
• 0
0
votes
6
replies
2.1k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 4.5 years ago by
Jovana Maksimovic
▴ 20 • written 5.5 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.4k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 4.5 years ago by
Jovana Maksimovic
▴ 20 • written 5.4 years ago by
stewart999
▴ 10
1
vote
2
replies
2.5k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 7.3 years ago by
James W. MacDonald
68k • written 7.3 years ago by
moldach
▴ 20
0
votes
0
replies
1.4k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
7.4 years ago
peter.fransquet
• 0
0
votes
0
replies
1.2k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
7.5 years ago
owen.whitley
▴ 10
0
votes
1
reply
1.9k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 7.6 years ago by
lhuang7
▴ 50 • written 8.6 years ago by
Simone
▴ 190
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
7.7 years ago
RC
• 0
0
votes
0
replies
1.5k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
7.7 years ago
Taub, Margaret
▴ 10
0
votes
2
replies
2.0k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 8.5 years ago by
Gordon Smyth
53k • written 8.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.8k
views
Details of gene names in DE
missmethyl
updated 8.8 years ago by
James W. MacDonald
68k • written 8.8 years ago by
r.clifford
• 0
0
votes
1
reply
1.7k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 8.8 years ago by
belinda.phipson
▴ 40 • written 8.9 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
2.1k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 9.4 years ago by
James W. MacDonald
68k • written 9.4 years ago by
graggsd
• 0
1
vote
3
replies
3.7k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.8 years ago
philipp24
▴ 30
3
votes
3
replies
4.5k
views
missMethyl: Gene ontology analysis
missMethyl
9.8 years ago
philipp24
▴ 30
0
votes
0
replies
1.6k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.8 years ago
philipp24
▴ 30
27 results • Page
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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