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missMethyl
•
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0
votes
0
replies
348
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
12 months ago
nurkenber
• 0
0
votes
1
reply
657
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
728
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 17 months ago by
nrenke
• 0 • written 17 months ago by
Lucie
• 0
1
vote
3
replies
2.3k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
23 months ago • updated 16 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 2.5 years ago by
Tim Peters
▴ 230 • written 2.5 years ago by
b.curran
• 0
0
votes
2
replies
1.2k
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 22 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
701
views
goMeth
missMethyl
2.9 years ago
anmolanp
▴ 10
2
votes
6
replies
1.8k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 2.9 years ago by
belinda.phipson
▴ 40 • written 2.9 years ago by
Joana
• 0
2
votes
3
replies
2.2k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 3.1 years ago by
belinda.phipson
▴ 40 • written 3.1 years ago by
Lukas
• 0
0
votes
6
replies
2.2k
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
1.5k
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 7.4 years ago by
James W. MacDonald
68k • written 7.4 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
7.6 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 7.7 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
1.6k
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
1.8k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 8.9 years ago by
belinda.phipson
▴ 40 • written 8.9 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
2.2k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 9.5 years ago by
James W. MacDonald
68k • written 9.5 years ago by
graggsd
• 0
1
vote
3
replies
3.8k
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
9.9 years ago • updated 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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Replies
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The linear model and design matrix that I described above is completely general. I imagine that it would be possible to use the same approa…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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