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minfi
•
reset
10
votes
3
replies
2.6k
views
minfi - estimateCellCount
minfi
8.8 years ago
Methyl
▴ 50
6
votes
3
replies
9.8k
views
Minfi issue: return code from pthread_create() is 22
minfi
450k
updated 14 months ago by
Sin
• 0 • written 4.8 years ago by
jshouse
▴ 10
6
votes
2
replies
4.2k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 7.4 years ago by
Dimitris Polychronopoulos
▴ 80 • written 8.1 years ago by
cardenasca
▴ 40
4
votes
10
replies
4.4k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 8.2 years ago by
Peter Hickey
▴ 740 • written 8.2 years ago by
Ahdee
▴ 50
4
votes
3
replies
1.8k
views
Discrepanices between minifi dmp finder and lmfit
illimina 450k methylation
minfi
limma
7.8 years ago
Andreas Paul
• 0
4
votes
1
reply
1.3k
views
An alternative to estimateCellCounts function
minfi
7.6 years ago • updated 7.4 years ago
Habil Zare
▴ 200
4
votes
4
replies
1.3k
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 5.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.2 years ago by
laurenz.holcik
• 0
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.1 years ago by
James W. MacDonald
65k • written 8.2 years ago by
AST
▴ 60
4
votes
8
replies
3.7k
views
minfi MethylationEPIC errors
minfi
methylation
IlluminaHumanMethylationEPICmanifest
IlluminaHumanMethylationEPICanno.ilmn10b.hg19
updated 8.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.1 years ago by
igor
▴ 40
4
votes
5
replies
5.9k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 6 months ago by
jay
• 0 • written 13 months ago by
luca.s
▴ 50
3
votes
6
replies
2.1k
views
Complex Model Design with Bumphunter (Minfi)
minfi
bumphunter
model.matrix
linear model
updated 13 months ago by
edward.esiribloom
• 0 • written 8.8 years ago by
andrew.j.skelton73
▴ 370
3
votes
7
replies
2.9k
views
estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
minfi
limma
updated 8.2 years ago by
Smeeta Shrestha
▴ 20 • written 8.8 years ago by
andrew.j.skelton73
▴ 370
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.1 years ago
rasii
• 0
3
votes
15
replies
6.4k
views
support for EPIC methylation arrays in minfi
minfi
updated 7.7 years ago by
line.heylen
▴ 10 • written 8.1 years ago by
Kasper Daniel Hansen
★ 6.5k
3
votes
3
replies
1.9k
views
Covert MethylSet to RGChannelSet object
minfi
hm450
updated 7.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.7 years ago by
metamaden
▴ 10
3
votes
2
replies
1.3k
views
Error when generate mapToGenome
minfi
GRanges
updated 6.4 years ago by
Peter Hickey
▴ 740 • written 6.4 years ago by
michaelwxf2012
• 0
3
votes
2
replies
460
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
4 months ago
kyj2226
• 0
3
votes
6
replies
1.7k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
Sophie Marion de Proce
• 0
2
votes
8
replies
4.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter
minfi
loading error
rtracklayer
updated 6.9 years ago by
nilan666
• 0 • written 7.0 years ago by
juan-pablo.cerapio-arroyo
▴ 10
2
votes
11
replies
9.2k
views
Minfi error in reading Basename column
methylation
minfi
updated 7.6 years ago by
SplittingInfinity
▴ 60 • written 8.7 years ago by
parap
• 0
2
votes
2
replies
1.3k
views
Problem installing Minfi on Cluster
Minfi
local installation
Centos
hpc
updated 6.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.0 years ago by
Goku
• 0
2
votes
2
replies
1.3k
views
limma for 450K methylation array data
limma
minfi
7.8 years ago
Andreas Paul
• 0
2
votes
1
reply
1.7k
views
smoothing function in bumphunter in minfi
minfi
bumphunter
minfi
bumphunter
updated 10.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.0 years ago by
Guest User
★ 13k
2
votes
1
reply
1.6k
views
Minfi: estimateCellCounts rgSet
minfi
450k
flowsorted.blood.450k
updated 7.4 years ago by
Habil Zare
▴ 200 • written 8.1 years ago by
cardenasca
▴ 40
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 4 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
2
votes
7
replies
2.2k
views
preprocessNoob + preprocessQuantile Error handling preprocessMethod
minfi
updated 8.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.7 years ago by
andrew.j.skelton73
▴ 370
2
votes
3
replies
935
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 16 months ago by
belinda.phipson
▴ 40 • written 16 months ago by
Lukas
• 0
2
votes
2
replies
2.5k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe
annotation
illimina 450k methylation
minfi
methylation
8.8 years ago
metamaden
▴ 10
2
votes
2
replies
871
views
How to overcome issue linked to loading big R object
minfi
R
methylation
3.0 years ago
Federica
▴ 10
2
votes
6
replies
1.9k
views
Bumphunting for longitudinal data
bumphunter
minfi
lmer
dmrcate
dmr analysis
updated 6.0 years ago by
Tim Peters
▴ 180 • written 6.0 years ago by
Ashlynn
• 0
1
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi
methylation
updated 19 months ago by
Sajad Wani
• 0 • written 6.8 years ago by
stewart999
▴ 10
1
vote
5
replies
2.4k
views
Meaning of the value column in bumphunter output (minfi package)
minfi
bumphunter
updated 6.2 years ago by
src3
• 0 • written 7.0 years ago by
Antonio M.
• 0
1
vote
3
replies
1.5k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
6.8 years ago
ezrabekele17
• 0
1
vote
2
replies
2.4k
views
read.metharray() not recognizing some of my EPIC arrays; force = TRUE not working either
minfi
7.1 years ago
Jenny Drnevich
★ 2.0k
1
vote
6
replies
1.9k
views
minfi and lumi not available for version 3.3.2
minfi
lumi
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Jessie.Johnson
▴ 10
1
vote
4
replies
4.2k
views
bumphunter output clarification
bumphunter
DMR
DMR analysis
minfi
bioconductor
updated 7.3 years ago by
rafa
▴ 60 • written 7.3 years ago by
chelsey.ju
• 0
1
vote
10
replies
3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi
lumi
methylumi
dmrcate
illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by
Tim Peters
▴ 180 • written 7.1 years ago by
poojitha.stemcell
▴ 10
1
vote
1
reply
1.5k
views
Minfi RGChannelSet preprocessing error in assayDataElement
minfi
preprocessing
error
updated 7.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.6 years ago by
lily
• 0
1
vote
3
replies
1.0k
views
Positions to genes in minfi
genomicranges
minfi
7.8 years ago • updated 7.7 years ago
Asma rabe
▴ 290
1
vote
1
reply
1.4k
views
Normalising GenomicMethylSet / MethylSet in Minfi
minfi
7.1 years ago
SplittingInfinity
▴ 60
1
vote
8
replies
3.3k
views
Normalization starting from beta values in minfi
methylation
minfi
written 7.9 years ago by
Asma rabe
▴ 290
1
vote
9
replies
2.7k
views
bumphunter beta values
methylation
minfi
bumphunter
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
igor
▴ 40
1
vote
1
reply
1.3k
views
Minfi User Guide Build Problem?
minfi
updated 7.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.9 years ago by
andrew.j.skelton73
▴ 370
1
vote
33
replies
4.1k
views
minfi failed positions in EPIC array
minfi
illuminahumanmethylationepicanno.ilmn10b.hg19
7.9 years ago • updated 7.8 years ago
Giovanni Calice
▴ 160
1
vote
6
replies
1.9k
views
Combining .idat and GEO data sets in minfi
minfi
8.0 years ago
matts
• 0
1
vote
1
reply
1.2k
views
minfi starting from beta values
minfi
8.0 years ago
Asma rabe
▴ 290
1
vote
2
replies
1.7k
views
minfi: error with estimateCellCounts
minfi
8.4 years ago
Brian Smith
▴ 120
1
vote
2
replies
1.6k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
7.8 years ago
m.van_iterson
▴ 20
1
vote
4
replies
2.1k
views
Help with DMPFinder in minfi package
Normalization
minfi
Normalization
minfi
updated 10.9 years ago by
James W. MacDonald
65k • written 10.9 years ago by
Srinivas Srikanth
▴ 70
1
vote
3
replies
2.0k
views
minfi - estimatecellcount function
minfi
illuminahumanmethylation450kanno.ilmn12.hg19
illuminahumanmethylation450k.db
updated 8.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.7 years ago by
AST
▴ 60
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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