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Minfi
•
reset
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
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
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
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
0
votes
8
replies
5.2k
views
Error using read.metharray.exp in minfi to read idat files
minfi
read.metharray.exp
idat
HM450k
6.5 years ago
poojitha.stemcell
▴ 10
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
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.1 years ago
rasii
• 0
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
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
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
33
replies
4.0k
views
minfi failed positions in EPIC array
minfi
illuminahumanmethylationepicanno.ilmn10b.hg19
7.8 years ago
Giovanni Calice
▴ 160
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
0
votes
0
replies
4.0k
views
Limma for DNA methylation arrays?
Normalization
probe
limma
minfi
Normalization
probe
limma
minfi
10.4 years ago
Gustavo Fernández Bayón
▴ 440
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
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 170 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
1
vote
2
replies
3.6k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 3.0 years ago by
sci_djw
• 0 • written 5.0 years ago by
researcher
• 0
0
votes
7
replies
3.6k
views
Weird things happening with minfi and RcppEigen
PROcess
minfi
PROcess
minfi
updated 11.4 years ago by
Benilton Carvalho
★ 4.3k • written 11.4 years ago by
Gustavo Fernández Bayón
▴ 440
1
vote
2
replies
3.5k
views
How do I remove bad samples/probes before normalization and SWAN?
Normalization
minfi
Normalization
minfi
updated 10.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.4 years ago by
Guest User
★ 13k
0
votes
5
replies
3.5k
views
doParallel with Bumphunter gives Error in mcfork()
minfi
bumphunter
minfi
bumphunter
updated 10.1 years ago by
Tim Triche
★ 4.2k • written 10.1 years ago by
Guest User
★ 13k
0
votes
2
replies
3.4k
views
minfi::read.metharray.exp error ("The following specified files do not exist")
minfi
read.metharray.exp
7.5 years ago
supermanrocketboy
▴ 10
1
vote
2
replies
3.3k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO
convert
minfi
bumphunter
GO
convert
minfi
bumphunter
updated 8.3 years ago by
david.watson
▴ 30 • written 10.0 years ago by
Guido Hooiveld
★ 3.9k
1
vote
7
replies
3.3k
views
Loading beta values into minfi
minfi
450k
updated 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
CC
▴ 10
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
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
6
replies
3.1k
views
difference in detection p-values from Minfi vs. GenomeStudio
minfi
genomestudio
methylation
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
brhead
▴ 40
0
votes
4
replies
3.0k
views
450k annotation packages compatible version and analysis with blockFinder (minfi)
Annotation
Clustering
convert
minfi
Annotation
Clustering
convert
minfi
updated 10.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.5 years ago by
Florence Cavalli
▴ 50
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
▴ 170 • written 7.1 years ago by
poojitha.stemcell
▴ 10
0
votes
6
replies
3.0k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Guest User
★ 13k
0
votes
7
replies
3.0k
views
Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
minfi
methylation
dmpfinder
limma
updated 7.0 years ago by
vulegom
• 0 • written 7.6 years ago by
mcall
▴ 20
0
votes
12
replies
2.9k
views
bumphunter DMRs difficulties
PROcess
minfi
bumphunter
PROcess
minfi
bumphunter
updated 10.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.2 years ago by
Giovanni Calice
▴ 160
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
0
votes
2
replies
2.9k
views
convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)
methylumi
minfi
methylumi
minfi
updated 12.2 years ago by
Tim Triche
★ 4.2k • written 12.2 years ago by
Aaron Mackey
▴ 170
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
1
vote
7
replies
2.8k
views
dmpFinder return value (minfi)
minfi
dmpfinder
dmp
illuminahumanmethylationepicanno.ilmn10b.hg19
epic microarray
updated 7.8 years ago by
James W. MacDonald
65k • written 7.8 years ago by
Biologist
▴ 110
0
votes
9
replies
2.8k
views
Rhdf5lib installation problem
minfi
Rhdf5lib
updated 3.3 years ago by
Mike Smith
★ 6.5k • written 3.3 years ago by
Giovanni Calice
▴ 160
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
Lin
▴ 50
1
vote
4
replies
2.7k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData
methy
Bioconductor
minfi
3.2 years ago
shweta
• 0
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
0
votes
2
replies
2.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 2.0 years ago by
Will
• 0 • written 8.6 years ago by
metamaden
▴ 10
1
vote
1
reply
2.7k
views
MethyLumiSet object
convert
genoset
minfi
convert
genoset
minfi
11.1 years ago
Tim Triche
★ 4.2k
10
votes
3
replies
2.6k
views
minfi - estimateCellCount
minfi
8.8 years ago
Methyl
▴ 50
0
votes
2
replies
2.6k
views
Full error messages?
minfi
minfi
12.0 years ago
Ed Siefker
▴ 230
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
0
votes
4
replies
2.4k
views
preprocessFunnorm in minfi
minfi
450k
illuminahumanmethylation450k.db
normalization
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
b.tawk
• 0
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
0
votes
4
replies
2.4k
views
minfi - how to subset a GenomicMethylSet by chromosome/seqname
Microarray
Annotation
PROcess
minfi
Microarray
Annotation
PROcess
minfi
updated 11.3 years ago by
Tim Triche
★ 4.2k • written 11.3 years ago by
Toby Hughes
▴ 30
0
votes
4
replies
2.4k
views
Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this object of class 'GenomicMethylSet'"?
minfi
updated 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
metamaden
▴ 10
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
0
votes
1
reply
2.2k
views
Analyzing 450k Methylation from TCGA Website
minfidata
minfi
illuminahumanmethylation450k.db
illuminahumanmethylation450kanno.ilmn12.hg19
9.0 years ago
alejandretheodore
• 0
0
votes
7
replies
2.2k
views
Use of minfi using (maverick3.2 and Developer) on Yosemite OS
version compatibility
minfi
9.1 years ago
morrisht
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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