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bumphunter
•
reset
0
votes
0
replies
90
views
Does bump hunter support Infinium Mouse Methylation BeadChip Array data?
bumphunter
11 weeks ago
ZHAOHUI
• 0
0
votes
9
replies
1.7k
views
clarification about bumphunter value output
minfi
bumphunter
updated 3 months ago by
terrybrownwork
• 0 • written 4.2 years ago by
src3
• 0
0
votes
4
replies
317
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
2.3 years ago
i.s.brorson
• 0
0
votes
2
replies
281
views
Bumphunter output "regions" of 1 probe (L =1)
DMR
bumphunter
EPIC chip
2.3 years ago
i.s.brorson
• 0
0
votes
1
reply
466
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi
bumphunter
Rsamtools
2.9 years ago
Boran Gao
• 0
2
votes
4
replies
655
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 3.0 years ago by
Yuan Tian
▴ 250 • written 3.0 years ago by
rasmus.rydbirk
▴ 10
6
votes
5
replies
663
views
dmrseq installation failed
installation problem
dmrseq
bumphunter
updated 3.5 years ago by
shepherl
3.1k • written 3.5 years ago by
guy.bioinfo
▴ 10
0
votes
3
replies
1.5k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation
minfi
bumphunter
updated 4.0 years ago by
Peter Hickey
▴ 550 • written 4.0 years ago by
muellerf
• 0
2
votes
6
replies
960
views
Bumphunting for longitudinal data
bumphunter
minfi
lmer
dmrcate
dmr analysis
updated 4.0 years ago by
Tim Peters
▴ 120 • written 4.0 years ago by
Ashlynn
• 0
0
votes
1
reply
714
views
Bumphunter error: subscript out of bounds
bumphunter
DMR
doparallel
multicore
4.0 years ago
arce.domingo.1407
• 0
1
vote
5
replies
1.5k
views
Meaning of the value column in bumphunter output (minfi package)
minfi
bumphunter
updated 4.2 years ago by
src3
• 0 • written 5.0 years ago by
Antonio M.
• 0
0
votes
0
replies
739
views
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
s4vectors
bumphunter
txdb.hsapiens.ucsc.hg38.knowngene
4.6 years ago
Leonardo Collado Torres
▴ 980
2
votes
8
replies
2.6k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter
minfi
loading error
rtracklayer
updated 5.0 years ago by
nilan666
• 0 • written 5.0 years ago by
juan-pablo.cerapio-arroyo
▴ 10
1
vote
3
replies
931
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 5.1 years ago by
James W. MacDonald
59k • written 5.1 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
1.3k
views
Controlling for confounding variables in bumphunter
minfi
bumphunter
confounders
updated 5.2 years ago by
James W. MacDonald
59k • written 5.2 years ago by
gft219
• 0
0
votes
1
reply
1.1k
views
"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
5.2 years ago
jon.barenboim
• 0
0
votes
0
replies
956
views
bumphunter P values and significance testing
minfi
bumphunter
5.2 years ago
cardenasca
▴ 40
4
votes
4
replies
1.9k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation
dmr analysis
bumphunter
updated 5.4 years ago by
James W. MacDonald
59k • written 5.4 years ago by
chelsey.ju
• 0
1
vote
4
replies
2.6k
views
bumphunter output clarification
bumphunter
DMR
DMR analysis
minfi
bioconductor
updated 5.4 years ago by
rafa
▴ 60 • written 5.4 years ago by
chelsey.ju
• 0
0
votes
4
replies
1.5k
views
Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi
sva
bumphunter
5.5 years ago • updated 5.4 years ago
brhead
▴ 40
6
votes
2
replies
3.0k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 5.4 years ago by
Dimitris Polychronopoulos
▴ 70 • written 6.2 years ago by
cardenasca
▴ 40
0
votes
0
replies
638
views
Bumphunter Algorithm Returns Regions with very few CpGs
bumphunter
minfi
5.6 years ago
graggsd
• 0
2
votes
6
replies
892
views
bumphunter of multi covariates
bumphunter
5.8 years ago
Asma rabe
▴ 290
0
votes
3
replies
692
views
minfi devel error
bumphunter
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
Asma rabe
▴ 290
0
votes
2
replies
673
views
Runing into error while trying GRanges from R
rnaseq
bumphunter
genomicranges
5.9 years ago
alva.james
• 0
0
votes
1
reply
742
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 5.9 years ago by
James W. MacDonald
59k • written 5.9 years ago by
fleur_p90
• 0
1
vote
9
replies
1.8k
views
bumphunter beta values
methylation
minfi
bumphunter
updated 6.1 years ago by
James W. MacDonald
59k • written 6.1 years ago by
igor
▴ 40
0
votes
0
replies
705
views
How to retrieve the (smoothed) baseline values from the bumphunting output object?
bumphunter
6.3 years ago
fabian.schroeder
• 0
1
vote
2
replies
2.5k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO
convert
minfi
bumphunter
GO
convert
minfi
bumphunter
updated 6.3 years ago by
david.watson
▴ 20 • written 8.0 years ago by
Guido Hooiveld
★ 3.2k
0
votes
3
replies
1.4k
views
Paired samples and interactions models with bumphunter?
minfi
bumphunter
design and contrast matrix
paired samples
limma
6.3 years ago
david.watson
▴ 20
1
vote
0
replies
755
views
News:
Bug found and fixed in bumphunter's bootstrap method
bumphunter
News
6.6 years ago
rafa
▴ 60
3
votes
5
replies
1.3k
views
Complex Model Design with Bumphunter (Minfi)
minfi
bumphunter
model.matrix
linear model
6.9 years ago
andrew.j.skelton73
▴ 360
0
votes
0
replies
598
views
Bumphunter Output Details
bumphunter
7.1 years ago
andrew.j.skelton73
▴ 360
4
votes
10
replies
2.0k
views
Using bumphunter with non-human genomes
bumphunter
updated 7.4 years ago by
Leonardo Collado Torres
▴ 980 • written 7.5 years ago by
jessica.hekman
▴ 40
3
votes
5
replies
1.5k
views
bumphunter::annotateNearest with non-human genome
bumphunter
updated 7.4 years ago by
Leonardo Collado Torres
▴ 980 • written 7.5 years ago by
jessica.hekman
▴ 40
2
votes
1
reply
1.5k
views
News:
Changes to matchGenes in bumphunter
annotation
bumphunter
News
updated 7.5 years ago by
Michael Love
37k • written 7.5 years ago by
rafa
▴ 60
0
votes
3
replies
1.5k
views
smoothing function in bumphunter in minfi
minfi
bumphunter
minfi
bumphunter
8.0 years ago • updated 7.9 years ago
Kasper Daniel Hansen
6.5k
0
votes
1
reply
1.2k
views
loessByCluster returning error in smooth function in bumphunter
bumphunter
bumphunter
8.0 years ago
Jiayi Sun
▴ 40
0
votes
0
replies
1.0k
views
minfi release 1.8
SNP
Annotation
GO
probe
SNPlocs
PROcess
minfi
bumphunter
ChAMP
SNP
Annotation
GO
probe
8.0 years ago
swarmqq@gmail.com
▴ 10
2
votes
1
reply
1.3k
views
smoothing function in bumphunter in minfi
minfi
bumphunter
minfi
bumphunter
updated 8.0 years ago by
Kasper Daniel Hansen
6.5k • written 8.0 years ago by
Guest User
★ 12k
0
votes
5
replies
2.7k
views
doParallel with Bumphunter gives Error in mcfork()
minfi
bumphunter
minfi
bumphunter
updated 8.1 years ago by
Tim Triche
★ 4.2k • written 8.1 years ago by
Guest User
★ 12k
0
votes
0
replies
1.2k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
8.2 years ago
Allegra Petti
▴ 120
0
votes
6
replies
2.2k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
updated 8.2 years ago by
James W. MacDonald
59k • written 8.2 years ago by
Guest User
★ 12k
0
votes
12
replies
2.0k
views
bumphunter DMRs difficulties
PROcess
minfi
bumphunter
PROcess
minfi
bumphunter
updated 8.3 years ago by
Kasper Daniel Hansen
6.5k • written 8.3 years ago by
Giovanni Calice
▴ 160
0
votes
3
replies
1.3k
views
minfi release 1.8
SNP
Annotation
GO
probe
SNPlocs
PROcess
minfi
bumphunter
ChAMP
SNP
Annotation
GO
probe
updated 8.3 years ago by
Smeeta Shrestha
▴ 20 • written 8.3 years ago by
Tim Triche
★ 4.2k
0
votes
0
replies
971
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
8.3 years ago
C T
▴ 20
0
votes
2
replies
1.6k
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
updated 8.5 years ago by
Kasper Daniel Hansen
6.5k • written 8.5 years ago by
Elmar Tobi
▴ 30
0
votes
1
reply
1.0k
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
updated 8.5 years ago by
Elmar Tobi
▴ 30 • written 8.5 years ago by
Kasper Daniel Hansen
6.5k
0
votes
5
replies
1.3k
views
bumphunter::matchGenes and all=TRUE
Annotation
bumphunter
Annotation
bumphunter
updated 8.8 years ago by
Kasper Daniel Hansen
6.5k • written 8.8 years ago by
Anne Biton
▴ 30
0
votes
0
replies
940
views
How to format SWAN minfi data for bumphunter?
minfi
bumphunter
minfi
bumphunter
8.9 years ago
Guest User
★ 12k
50 results • Page
1 of 1
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Replies
Comment: ashr vs apeglm for interaction data
by
Ali Barry
▴ 30
Thanks, I'll trying playing a bit there. I have done some minor filtering already (requiring at least 5 counts in 10% of my samples, across…
Comment: ashr vs apeglm for interaction data
by
Michael Love
37k
I see why apeglm is conservative— the dispersion is very high within group. An idea would be to use ashr but do some additional filtering …
Comment: How to figure out the FC value from Limma
by
ATpoint
★ 1.2k
That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.
Comment: ashr vs apeglm for interaction data
by
Ali Barry
▴ 30
Hi Michael, Plots attached. Many of the large fold changes with `ashr` are driven by one sample per group, but a few are maybe a bit more …
Comment: regression analysis for epic array methylation data using limma
by
nabiyogesh
▴ 10
Thanks! I have tried this; I am not sure after that how to find logeGFR associated probe? and also, how to filter significant probe? …
Votes
Answer: How to properly use DESeq2 for an experiment
Comment: ashr vs apeglm for interaction data
Comment: How to figure out the FC value from Limma
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
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