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missmethyl
•
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0
votes
0
replies
293
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
9 months ago
nurkenber
• 0
0
votes
1
reply
512
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
maximuscfyeung
• 0
0
votes
2
replies
555
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
maximuscfyeung
• 0
0
votes
2
replies
977
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 14 months ago by
nrenke
• 0 • written 14 months ago by
Lucie
• 0
1
vote
3
replies
2.1k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
19 months ago • updated 13 months ago
s.malik
• 0
0
votes
1
reply
1.1k
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 2.2 years ago by
Tim Peters
▴ 230 • written 2.2 years ago by
b.curran
• 0
0
votes
2
replies
1.1k
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 19 months ago by
CHEN
• 0 • written 2.4 years ago by
Saanchi
• 0
1
vote
1
reply
1.0k
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 2.5 years ago by
belinda.phipson
▴ 40 • written 2.5 years ago by
Grace
• 0
0
votes
1
reply
939
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
2.5 years ago
Grace
• 0
0
votes
0
replies
617
views
goMeth
missMethyl
2.6 years ago
anmolanp
▴ 10
2
votes
6
replies
1.7k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 2.6 years ago by
belinda.phipson
▴ 40 • written 2.6 years ago by
Joana
• 0
2
votes
3
replies
2.0k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.8 years ago by
belinda.phipson
▴ 40 • written 2.8 years ago by
Lukas
• 0
0
votes
6
replies
2.0k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 4.3 years ago by
Jovana Maksimovic
▴ 20 • written 5.3 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.3k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 4.3 years ago by
Jovana Maksimovic
▴ 20 • written 5.2 years ago by
stewart999
▴ 10
1
vote
2
replies
2.5k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
moldach
▴ 20
0
votes
0
replies
1.3k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
7.2 years ago
peter.fransquet
• 0
0
votes
0
replies
1.2k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
7.3 years ago
owen.whitley
▴ 10
0
votes
1
reply
1.8k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 7.4 years ago by
lhuang7
▴ 50 • written 8.3 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
7.5 years ago
RC
• 0
0
votes
0
replies
1.3k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
7.5 years ago
Taub, Margaret
▴ 10
0
votes
2
replies
1.9k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 8.3 years ago by
Gordon Smyth
53k • written 8.4 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.7k
views
Details of gene names in DE
missmethyl
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
r.clifford
• 0
0
votes
1
reply
1.7k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 8.6 years ago by
belinda.phipson
▴ 40 • written 8.6 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
2.0k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 9.2 years ago by
James W. MacDonald
68k • written 9.2 years ago by
graggsd
• 0
1
vote
3
replies
3.6k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.6 years ago
philipp24
▴ 30
3
votes
3
replies
4.3k
views
missMethyl: Gene ontology analysis
missMethyl
9.6 years ago
philipp24
▴ 30
0
votes
0
replies
1.5k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.6 years ago
philipp24
▴ 30
27 results • Page
1 of 1
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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