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methylation
•
reset
1
vote
2
replies
800
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
3 months ago • updated 12 weeks ago
Kim
• 0
0
votes
1
reply
267
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
ja569116
• 0
1
vote
8
replies
725
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 5 months ago by
Gordon Smyth
51k • written 6 months ago by
sat
• 0
0
votes
0
replies
376
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
7 months ago
kyj2226
• 0
1
vote
3
replies
1.6k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 8 months ago by
Robert Ivanek
▴ 740 • written 3.2 years ago by
ltzhou
• 0
0
votes
7
replies
2.0k
views
error with champ.load
ChAMP
champ
methylation
updated 11 months ago by
mike
• 0 • written 4.3 years ago by
jkong
• 0
0
votes
2
replies
863
views
error in champ.SVD
svd
methylation
champ
updated 15 months ago by
shepherl
3.9k • written 15 months ago by
Giulia
• 0
1
vote
0
replies
643
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
2.0 years ago
hlee
▴ 10
2
votes
1
reply
718
views
Limma model orientation
limma
methylation
MethylationArray
updated 2.2 years ago by
James W. MacDonald
66k • written 2.2 years ago by
fluentin44
• 0
0
votes
2
replies
2.9k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 2.2 years ago by
Will
• 0 • written 8.8 years ago by
metamaden
▴ 10
1
vote
1
reply
845
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 2.4 years ago by
tcalvo
▴ 90 • written 2.4 years ago by
megha.hs28
▴ 10
0
votes
0
replies
787
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
2.5 years ago
Lorenzo
• 0
0
votes
1
reply
1.3k
views
Gene level methylation values
methylation
methylKit
bsseq
updated 2.8 years ago by
alex.gos90
▴ 10 • written 3.0 years ago by
ag1805x
▴ 80
2
votes
2
replies
934
views
How to overcome issue linked to loading big R object
minfi
R
methylation
3.2 years ago
Federica
▴ 10
1
vote
5
replies
4.5k
views
minfi - error when reading idat files
minfi
methylation
updated 22 months ago by
Sajad Wani
• 0 • written 7.1 years ago by
stewart999
▴ 10
0
votes
0
replies
1.0k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.5 years ago
epibio
▴ 10
0
votes
1
reply
932
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation
epigenomics
slurm
mpi
methylmix
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
parra.sev
▴ 20
0
votes
0
replies
800
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.0 years ago
i.s.castanho
• 0
0
votes
1
reply
693
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.2 years ago
AishaD
• 0
2
votes
1
reply
1.1k
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
4.3 years ago
Zach Roe
▴ 10
0
votes
0
replies
955
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
4.3 years ago
marcin.bazyliszek
• 0
0
votes
1
reply
663
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.3 years ago
i.s.castanho
• 0
1
vote
1
reply
1.0k
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 4.4 years ago by
James W. MacDonald
66k • written 4.4 years ago by
whyw6948
• 0
0
votes
4
replies
991
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
4.5 years ago
i.s.brorson
• 0
1
vote
3
replies
1.5k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.5 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
877
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 4.5 years ago by
Yuan Tian
▴ 90 • written 4.5 years ago by
cherlyn.t
• 0
0
votes
0
replies
774
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.5 years ago
A
▴ 40
0
votes
1
reply
2.9k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
4.6 years ago
ph.shimaasherif
• 0
2
votes
16
replies
2.8k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 4.6 years ago by
Yuan Tian
▴ 290 • written 4.6 years ago by
Ankit
▴ 20
0
votes
8
replies
1.1k
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
4.6 years ago
sara.blocquiaux
• 0
0
votes
0
replies
734
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
4.6 years ago
luciomora8
• 0
0
votes
1
reply
1.1k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
lucasmiranda42
• 0
1
vote
3
replies
1.1k
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 4.7 years ago by
James W. MacDonald
66k • written 4.7 years ago by
yuabrahamliu
• 0
1
vote
3
replies
1.1k
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
4.7 years ago
patriciasolesanchez
• 0
0
votes
1
reply
757
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
4.8 years ago
sorjuelal
• 0
0
votes
2
replies
922
views
Illumina 450K quality controls with meffil
meffil
EWAS
methylation
updated 4.8 years ago by
James W. MacDonald
66k • written 4.8 years ago by
uxue33
• 0
3
votes
5
replies
1.5k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 4.8 years ago by
James W. MacDonald
66k • written 4.8 years ago by
yoursbassanio
▴ 10
0
votes
0
replies
786
views
DSS for non-CpG site analysis
DSS
methylation
4.9 years ago
CalM
• 0
0
votes
4
replies
1.7k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 18 months ago by
shuo
• 0 • written 4.9 years ago by
enora.fremy
• 0
1
vote
3
replies
1.6k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 4.9 years ago by
tgorri
▴ 10 • written 4.9 years ago by
sara.blocquiaux
• 0
1
vote
6
replies
1.9k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.9 years ago
sabrina.mcnew
• 0
1
vote
2
replies
3.9k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 3.3 years ago by
sci_djw
• 0 • written 5.2 years ago by
researcher
• 0
1
vote
4
replies
1.6k
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 5.1 years ago by
keegan
▴ 60 • written 5.1 years ago by
sorjuelal
• 0
0
votes
2
replies
2.2k
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 8 months ago by
peter.brederlo
• 0 • written 5.2 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
5.3 years ago
gerald.mccollam
• 0
4
votes
4
replies
1.4k
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 5.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.4 years ago by
laurenz.holcik
• 0
0
votes
0
replies
1.2k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
5.5 years ago • updated 5.4 years ago
moldach
▴ 20
0
votes
1
reply
1.0k
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 5.5 years ago by
James W. MacDonald
66k • written 5.5 years ago by
lalchungnungabt17
• 0
1
vote
2
replies
1.5k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 5.6 years ago by
Ou, Jianhong
★ 1.3k • written 5.6 years ago by
Adam_M
• 0
2
votes
1
reply
1.4k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 5.7 years ago by
Yuan Tian
▴ 290 • written 5.7 years ago by
D
▴ 10
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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