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Showing :
methylation
•
reset
0
votes
0
replies
149
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
6 months ago
hlee
• 0
2
votes
1
reply
234
views
Limma model orientation
limma
methylation
MethylationArray
updated 8 months ago by
James W. MacDonald
62k • written 8 months ago by
fluentin44
• 0
0
votes
2
replies
1.9k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 9 months ago by
Will
• 0 • written 7.3 years ago by
metamaden
▴ 10
1
vote
1
reply
309
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 10 months ago by
tcalvo
▴ 80 • written 10 months ago by
megha.hs28
▴ 10
0
votes
0
replies
272
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
11 months ago
Lorenzo
• 0
0
votes
1
reply
430
views
Gene level methylation values
methylation
methylKit
bsseq
updated 15 months ago by
alex.gos90
▴ 10 • written 18 months ago by
ag1805x
▴ 50
1
vote
1
reply
534
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 21 months ago by
Robert Ivanek
▴ 730 • written 21 months ago by
ltzhou
• 0
2
votes
2
replies
456
views
How to overcome issue linked to loading big R object
minfi
R
methylation
21 months ago
Federica
▴ 10
1
vote
5
replies
2.5k
views
minfi - error when reading idat files
minfi
methylation
updated 4 months ago by
Sajad Wani
• 0 • written 5.6 years ago by
stewart999
▴ 10
0
votes
0
replies
565
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
2.0 years ago
epibio
▴ 10
0
votes
1
reply
453
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation
epigenomics
slurm
mpi
methylmix
updated 2.5 years ago by
Kevin Blighe
3.7k • written 2.5 years ago by
parra.sev
▴ 20
0
votes
0
replies
348
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
2.5 years ago
i.s.castanho
• 0
0
votes
1
reply
309
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
2.7 years ago
AishaD
• 0
2
votes
1
reply
505
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
2.8 years ago
Zach Roe
▴ 10
0
votes
0
replies
462
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
2.8 years ago
marcin.bazyliszek
• 0
0
votes
6
replies
805
views
error with champ.load
ChAMP
champ
methylation
updated 18 months ago by
Nidhi
• 0 • written 2.8 years ago by
jkong
• 0
0
votes
1
reply
288
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
2.8 years ago
i.s.castanho
• 0
1
vote
1
reply
495
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 2.9 years ago by
James W. MacDonald
62k • written 2.9 years ago by
whyw6948
• 0
0
votes
4
replies
448
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
3.0 years ago
i.s.brorson
• 0
1
vote
3
replies
769
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
3.0 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
472
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 3.0 years ago by
Yuan Tian
▴ 90 • written 3.0 years ago by
cherlyn.t
• 0
0
votes
0
replies
329
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
3.0 years ago
A
▴ 40
0
votes
1
reply
1.8k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
3.1 years ago
ph.shimaasherif
• 0
2
votes
16
replies
1.3k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 3.1 years ago by
Yuan Tian
▴ 250 • written 3.1 years ago by
Ankit
▴ 10
0
votes
8
replies
504
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
3.1 years ago
sara.blocquiaux
• 0
0
votes
0
replies
367
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
3.1 years ago
luciomora8
• 0
0
votes
1
reply
522
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 3.1 years ago by
Kevin Blighe
3.7k • written 3.1 years ago by
lucasmiranda42
• 0
1
vote
3
replies
593
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 3.2 years ago by
James W. MacDonald
62k • written 3.2 years ago by
yuabrahamliu
• 0
1
vote
3
replies
546
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
3.2 years ago
patriciasolesanchez
• 0
0
votes
1
reply
368
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
3.3 years ago
sorjuelal
• 0
0
votes
2
replies
510
views
Illumina 450K quality controls with meffil
meffil
EWAS
methylation
updated 3.3 years ago by
James W. MacDonald
62k • written 3.3 years ago by
uxue33
• 0
3
votes
5
replies
691
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 3.3 years ago by
James W. MacDonald
62k • written 3.3 years ago by
yoursbassanio
▴ 10
0
votes
0
replies
356
views
DSS for non-CpG site analysis
DSS
methylation
3.4 years ago
CalM
• 0
0
votes
4
replies
830
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 10 days ago by
shuo
• 0 • written 3.4 years ago by
enora.fremy
• 0
1
vote
3
replies
860
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 3.4 years ago by
tgorri
▴ 10 • written 3.4 years ago by
sara.blocquiaux
• 0
1
vote
6
replies
786
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
3.4 years ago
sabrina.mcnew
• 0
1
vote
2
replies
2.2k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 21 months ago by
sci_djw
• 0 • written 3.7 years ago by
researcher
• 0
1
vote
4
replies
825
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 3.6 years ago by
keegan
▴ 60 • written 3.6 years ago by
sorjuelal
• 0
0
votes
1
reply
1.1k
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 3.7 years ago by
Yuan Tian
▴ 250 • written 3.7 years ago by
moldach
▴ 20
0
votes
0
replies
824
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks
SummarizedExperiment
TCGAanalyze_DMR
methylation
R
3.8 years ago
gerald.mccollam
• 0
4
votes
4
replies
728
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 3.9 years ago by
Kasper Daniel Hansen
6.5k • written 3.9 years ago by
laurenz.holcik
• 0
0
votes
0
replies
722
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
4.0 years ago • updated 3.9 years ago
moldach
▴ 20
0
votes
1
reply
545
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 4.0 years ago by
James W. MacDonald
62k • written 4.0 years ago by
lalchungnungabt17
• 0
1
vote
2
replies
937
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 4.1 years ago by
Ou, Jianhong
★ 1.3k • written 4.1 years ago by
Adam_M
• 0
2
votes
1
reply
807
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 4.2 years ago by
Yuan Tian
▴ 250 • written 4.2 years ago by
D
• 0
0
votes
0
replies
480
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
4.2 years ago
saripalligautam86
▴ 10
0
votes
2
replies
1.5k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP
Normalization
FunctionalNormalization
methylation
EPIC
4.3 years ago
yuabrahamliu
• 0
1
vote
2
replies
1.4k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 4.4 years ago by
James W. MacDonald
62k • written 4.4 years ago by
moldach
▴ 20
2
votes
8
replies
1.1k
views
edgeR: design matrix for methylation analysis
edger
methylation
updated 4.4 years ago by
Gordon Smyth
47k • written 4.6 years ago by
sgld
• 0
0
votes
0
replies
589
views
Error while using TCGAanalyze_DMR for >2 groups
methylation
tcgabiolinks
R
gleason score
TCGAanalyze_DMR
4.4 years ago
mtkk94
• 0
50 results • Page
1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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