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Methylation
•
reset
1
vote
2
replies
327
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
267
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
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
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
1.4k
views
Error processing Infinium 450K Methylation data using Minfi
minfi
software error
methylation
illumina450k
updated 11 months ago by
kuzn.di
• 0 • written 8.4 years ago by
pm2015
• 0
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
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
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
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
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
1
vote
9
replies
3.6k
views
strange results from differential methylation analysis using limma
limma
methylation
methyanalysis
IMA
updated 24 months ago by
Sean Davis
21k • written 7.2 years ago by
RC
• 0
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
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
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
699
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
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
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
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
50 results • Page
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Replies
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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