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Showing :
Methylation
•
reset
1
vote
2
replies
322
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 6 days ago
Kim
• 0
0
votes
1
reply
165
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
ja569116
• 0
1
vote
8
replies
552
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
0
replies
266
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
4 months ago
kyj2226
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
0
votes
7
replies
1.8k
views
error with champ.load
ChAMP
champ
methylation
updated 8 months ago by
mike
• 0 • written 4.1 years ago by
jkong
• 0
0
votes
2
replies
758
views
error in champ.SVD
svd
methylation
champ
updated 13 months ago by
shepherl
3.9k • written 13 months ago by
Giulia
• 0
1
vote
0
replies
578
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
22 months ago
hlee
▴ 10
2
votes
1
reply
658
views
Limma model orientation
limma
methylation
MethylationArray
updated 2.0 years ago by
James W. MacDonald
65k • written 2.0 years ago by
fluentin44
• 0
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
784
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 2.2 years ago by
tcalvo
▴ 90 • written 2.2 years ago by
megha.hs28
▴ 10
0
votes
0
replies
736
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
2.3 years ago
Lorenzo
• 0
0
votes
1
reply
1.1k
views
Gene level methylation values
methylation
methylKit
bsseq
updated 2.6 years ago by
alex.gos90
▴ 10 • written 2.8 years ago by
ag1805x
▴ 80
2
votes
2
replies
874
views
How to overcome issue linked to loading big R object
minfi
R
methylation
3.0 years ago
Federica
▴ 10
1
vote
5
replies
4.2k
views
minfi - error when reading idat files
minfi
methylation
updated 20 months ago by
Sajad Wani
• 0 • written 6.8 years ago by
stewart999
▴ 10
0
votes
0
replies
971
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.3 years ago
epibio
▴ 10
0
votes
1
reply
869
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation
epigenomics
slurm
mpi
methylmix
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
parra.sev
▴ 20
0
votes
0
replies
752
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
3.8 years ago
i.s.castanho
• 0
0
votes
1
reply
646
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.0 years ago
AishaD
• 0
2
votes
1
reply
995
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
4.0 years ago
Zach Roe
▴ 10
0
votes
0
replies
884
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
4.1 years ago
marcin.bazyliszek
• 0
0
votes
1
reply
612
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.1 years ago
i.s.castanho
• 0
1
vote
1
reply
951
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
whyw6948
• 0
0
votes
4
replies
919
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
4.3 years ago • updated 4.2 years ago
i.s.brorson
• 0
1
vote
3
replies
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.3 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
825
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 4.3 years ago by
Yuan Tian
▴ 90 • written 4.3 years ago by
cherlyn.t
• 0
0
votes
0
replies
705
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.3 years ago
A
▴ 40
0
votes
1
reply
2.8k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
4.3 years ago
ph.shimaasherif
• 0
2
votes
16
replies
2.6k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 4.3 years ago by
Yuan Tian
▴ 280 • written 4.3 years ago by
Ankit
▴ 20
0
votes
8
replies
1.0k
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
4.3 years ago
sara.blocquiaux
• 0
0
votes
0
replies
677
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
4.3 years ago
luciomora8
• 0
0
votes
1
reply
981
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.4 years ago by
lucasmiranda42
• 0
1
vote
3
replies
1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
yuabrahamliu
• 0
1
vote
3
replies
1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
4.5 years ago
patriciasolesanchez
• 0
0
votes
1
reply
698
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
4.5 years ago
sorjuelal
• 0
0
votes
2
replies
859
views
Illumina 450K quality controls with meffil
meffil
EWAS
methylation
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
uxue33
• 0
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
yoursbassanio
▴ 10
0
votes
0
replies
732
views
DSS for non-CpG site analysis
DSS
methylation
4.6 years ago
CalM
• 0
0
votes
4
replies
1.6k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 15 months ago by
shuo
• 0 • written 4.7 years ago by
enora.fremy
• 0
1
vote
3
replies
1.5k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 4.7 years ago by
tgorri
▴ 10 • written 4.7 years ago by
sara.blocquiaux
• 0
1
vote
6
replies
1.7k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.7 years ago
sabrina.mcnew
• 0
1
vote
2
replies
3.6k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 3.1 years ago by
sci_djw
• 0 • written 5.0 years ago by
researcher
• 0
1
vote
4
replies
1.5k
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 4.9 years ago by
keegan
▴ 60 • written 4.9 years ago by
sorjuelal
• 0
0
votes
2
replies
2.0k
views
ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP
methylation
BMIQ
updated 6 months ago by
peter.brederlo
• 0 • written 5.0 years ago by
moldach
▴ 20
0
votes
0
replies
1.3k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks
SummarizedExperiment
TCGAanalyze_DMR
methylation
R
5.1 years ago
gerald.mccollam
• 0
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
0
votes
0
replies
1.1k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
5.2 years ago
moldach
▴ 20
0
votes
1
reply
929
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
lalchungnungabt17
• 0
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 5.4 years ago by
Ou, Jianhong
★ 1.3k • written 5.4 years ago by
Adam_M
• 0
2
votes
1
reply
1.3k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 5.5 years ago by
Yuan Tian
▴ 280 • written 5.5 years ago by
D
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold
by
j.gilbert
• 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Votes
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
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