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missmethyl
•
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0
votes
0
replies
61
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
6 days ago
nurkenber
• 0
0
votes
1
reply
79
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 13 days ago by
James W. MacDonald
67k • written 13 days ago by
maximuscfyeung
• 0
0
votes
2
replies
245
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 14 days ago by
James W. MacDonald
67k • written 14 days ago by
maximuscfyeung
• 0
0
votes
2
replies
550
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 5 months ago by
nrenke
• 0 • written 5 months ago by
Lucie
• 0
1
vote
3
replies
1.6k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
10 months ago • updated 4 months ago
s.malik
• 0
0
votes
1
reply
802
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 17 months ago by
Tim Peters
▴ 200 • written 17 months ago by
b.curran
• 0
0
votes
2
replies
832
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 10 months ago by
CHEN
• 0 • written 20 months ago by
Saanchi
• 0
1
vote
1
reply
806
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 20 months ago by
belinda.phipson
▴ 40 • written 21 months ago by
Grace
• 0
0
votes
1
reply
714
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
21 months ago
Grace
• 0
0
votes
0
replies
518
views
goMeth
missMethyl
22 months ago
anmolanp
▴ 10
2
votes
6
replies
1.3k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 22 months ago by
belinda.phipson
▴ 40 • written 22 months ago by
Joana
• 0
2
votes
3
replies
1.5k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.0 years ago by
belinda.phipson
▴ 40 • written 2.0 years ago by
Lukas
• 0
0
votes
6
replies
1.6k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 3.5 years ago by
Jovana Maksimovic
▴ 20 • written 4.5 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.1k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 3.5 years ago by
Jovana Maksimovic
▴ 20 • written 4.4 years ago by
stewart999
▴ 10
1
vote
2
replies
2.3k
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
6.4 years ago
peter.fransquet
• 0
0
votes
0
replies
1.0k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
6.6 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 6.7 years ago by
lhuang7
▴ 50 • written 7.6 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
6.7 years ago
RC
• 0
0
votes
0
replies
1.1k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
6.7 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 7.5 years ago by
Gordon Smyth
52k • written 7.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.5k
views
Details of gene names in DE
missmethyl
updated 7.8 years ago by
James W. MacDonald
67k • written 7.8 years ago by
r.clifford
• 0
0
votes
1
reply
1.4k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 7.9 years ago by
belinda.phipson
▴ 40 • written 7.9 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
1.7k
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
8.8 years ago
philipp24
▴ 30
3
votes
3
replies
3.9k
views
missMethyl: Gene ontology analysis
missMethyl
8.9 years ago • updated 8.8 years ago
philipp24
▴ 30
0
votes
0
replies
1.4k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
8.8 years ago
philipp24
▴ 30
27 results • Page
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Comment: EdgeR Biological CVs
by
ATpoint
★ 4.6k
"Joseph" is a spam bot...
Comment: Problems with oarfish + tximport + swish
by
Im
• 0
Office ta kemon
Answer: How to sort negative log2FC or FC in RNAseq for GSEA?
by
ATpoint
★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs
by
James
• 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Comment: EdgeR Biological CVs
by
Joseph
▴ 10
I believe the published study provides answers to your questions. Yunshun Chen and Pedro Baldoni's recent papers on edgeR may also be of in…
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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