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missmethyl
•
reset
0
votes
0
replies
160
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
3 months ago
nurkenber
• 0
0
votes
1
reply
304
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
maximuscfyeung
• 0
0
votes
2
replies
394
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
maximuscfyeung
• 0
0
votes
2
replies
758
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 8 months ago by
nrenke
• 0 • written 8 months ago by
Lucie
• 0
1
vote
3
replies
1.9k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
13 months ago • updated 7 months ago
s.malik
• 0
0
votes
1
reply
912
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 20 months ago by
Tim Peters
▴ 230 • written 20 months ago by
b.curran
• 0
0
votes
2
replies
909
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 13 months ago by
CHEN
• 0 • written 23 months ago by
Saanchi
• 0
1
vote
1
reply
886
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 24 months ago by
belinda.phipson
▴ 40 • written 24 months ago by
Grace
• 0
0
votes
1
reply
800
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
24 months ago
Grace
• 0
0
votes
0
replies
553
views
goMeth
missMethyl
2.1 years ago
anmolanp
▴ 10
2
votes
6
replies
1.5k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 2.1 years ago by
belinda.phipson
▴ 40 • written 2.1 years ago by
Joana
• 0
2
votes
3
replies
1.7k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.3 years ago by
belinda.phipson
▴ 40 • written 2.3 years ago by
Lukas
• 0
0
votes
6
replies
1.7k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 3.8 years ago by
Jovana Maksimovic
▴ 20 • written 4.8 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.2k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 3.8 years ago by
Jovana Maksimovic
▴ 20 • written 4.6 years ago by
stewart999
▴ 10
1
vote
2
replies
2.3k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 6.6 years ago by
James W. MacDonald
68k • written 6.6 years ago by
moldach
▴ 20
0
votes
0
replies
1.2k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
6.7 years ago
peter.fransquet
• 0
0
votes
0
replies
1.1k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
6.8 years ago
owen.whitley
▴ 10
0
votes
1
reply
1.7k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 6.9 years ago by
lhuang7
▴ 50 • written 7.8 years ago by
Simone
▴ 190
0
votes
0
replies
1.2k
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
7.0 years ago
RC
• 0
0
votes
0
replies
1.2k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
7.0 years ago
Taub, Margaret
▴ 10
0
votes
2
replies
1.7k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 7.8 years ago by
Gordon Smyth
52k • written 7.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.5k
views
Details of gene names in DE
missmethyl
updated 8.1 years ago by
James W. MacDonald
68k • written 8.1 years ago by
r.clifford
• 0
0
votes
1
reply
1.5k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 8.1 years ago by
belinda.phipson
▴ 40 • written 8.1 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
1.8k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
graggsd
• 0
1
vote
3
replies
3.5k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.1 years ago
philipp24
▴ 30
3
votes
3
replies
4.1k
views
missMethyl: Gene ontology analysis
missMethyl
9.1 years ago
philipp24
▴ 30
0
votes
0
replies
1.4k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.1 years ago
philipp24
▴ 30
27 results • Page
1 of 1
Recent ...
Replies
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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