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missMethyl
•
reset
0
votes
0
replies
177
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
4 months ago
nurkenber
• 0
0
votes
1
reply
352
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
maximuscfyeung
• 0
0
votes
2
replies
419
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
maximuscfyeung
• 0
0
votes
2
replies
801
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 8 months ago by
nrenke
• 0 • written 9 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
14 months ago • updated 8 months ago
s.malik
• 0
0
votes
1
reply
936
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 21 months ago by
Tim Peters
▴ 230 • written 21 months ago by
b.curran
• 0
0
votes
2
replies
923
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 13 months ago by
CHEN
• 0 • written 2.0 years ago by
Saanchi
• 0
1
vote
1
reply
903
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 2.0 years ago by
belinda.phipson
▴ 40 • written 2.0 years ago by
Grace
• 0
0
votes
1
reply
810
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
2.1 years ago
Grace
• 0
0
votes
0
replies
557
views
goMeth
missMethyl
2.2 years ago
anmolanp
▴ 10
2
votes
6
replies
1.5k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 2.2 years ago by
belinda.phipson
▴ 40 • written 2.2 years ago by
Joana
• 0
2
votes
3
replies
1.8k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.4 years ago by
belinda.phipson
▴ 40 • written 2.4 years ago by
Lukas
• 0
0
votes
6
replies
1.8k
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 4.7 years ago by
stewart999
▴ 10
1
vote
2
replies
2.3k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 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
6.9 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 7.0 years ago by
lhuang7
▴ 50 • written 7.9 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 8.0 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 8.2 years ago by
belinda.phipson
▴ 40 • written 8.2 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 8.8 years ago by
James W. MacDonald
68k • written 8.8 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
9.2 years ago • updated 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: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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caroline.zanchi
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