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missmethyl
•
reset
0
votes
2
replies
497
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 4 months ago by
nrenke
• 0 • written 4 months ago by
Lucie
• 0
1
vote
3
replies
1.5k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
9 months ago • updated 3 months ago
s.malik
• 0
0
votes
1
reply
777
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 16 months ago by
Tim Peters
▴ 200 • written 16 months ago by
b.curran
• 0
0
votes
2
replies
809
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 9 months ago by
CHEN
• 0 • written 19 months ago by
Saanchi
• 0
1
vote
1
reply
788
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 19 months ago by
belinda.phipson
▴ 40 • written 19 months ago by
Grace
• 0
0
votes
1
reply
692
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
20 months ago
Grace
• 0
0
votes
0
replies
508
views
goMeth
missMethyl
21 months ago
anmolanp
▴ 10
2
votes
6
replies
1.3k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 21 months ago by
belinda.phipson
▴ 40 • written 21 months ago by
Joana
• 0
2
votes
3
replies
1.4k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 23 months ago by
belinda.phipson
▴ 40 • written 23 months ago by
Lukas
• 0
0
votes
6
replies
1.6k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 3.4 years ago by
Jovana Maksimovic
▴ 20 • written 4.4 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.1k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 3.4 years ago by
Jovana Maksimovic
▴ 20 • written 4.3 years ago by
stewart999
▴ 10
1
vote
2
replies
2.2k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 6.3 years ago by
James W. MacDonald
67k • written 6.3 years ago by
moldach
▴ 20
0
votes
0
replies
1.1k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
6.3 years ago
peter.fransquet
• 0
0
votes
0
replies
1.0k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
6.5 years ago
owen.whitley
▴ 10
0
votes
1
reply
1.6k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 6.6 years ago by
lhuang7
▴ 50 • written 7.5 years ago by
Simone
▴ 190
0
votes
0
replies
1.1k
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
6.6 years ago
RC
• 0
0
votes
0
replies
1.1k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
6.6 years ago
Taub, Margaret
▴ 10
0
votes
2
replies
1.6k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 7.4 years ago by
Gordon Smyth
52k • written 7.6 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.4k
views
Details of gene names in DE
missmethyl
updated 7.7 years ago by
James W. MacDonald
67k • written 7.7 years ago by
r.clifford
• 0
0
votes
1
reply
1.4k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 7.8 years ago by
belinda.phipson
▴ 40 • written 7.8 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
1.6k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 8.4 years ago by
James W. MacDonald
67k • written 8.4 years ago by
graggsd
• 0
1
vote
3
replies
3.3k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
8.7 years ago
philipp24
▴ 30
3
votes
3
replies
3.9k
views
missMethyl: Gene ontology analysis
missMethyl
8.8 years ago • updated 8.7 years ago
philipp24
▴ 30
0
votes
0
replies
1.4k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
8.7 years ago
philipp24
▴ 30
24 results • Page
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Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation. Like most classical linear modeling procedures in statistics, limma uses a statistical model to represen…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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Ali Barry
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James W. MacDonald
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