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Showing :
Methylation
•
reset
0
votes
2
replies
177
views
error in champ.SVD
svd
methylation
champ
updated 7 weeks ago by
shepherl
3.5k • written 7 weeks ago by
Giulia
• 0
1
vote
0
replies
231
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
10 months ago
hlee
▴ 10
2
votes
1
reply
359
views
Limma model orientation
limma
methylation
MethylationArray
updated 13 months ago by
James W. MacDonald
63k • written 13 months ago by
fluentin44
• 0
0
votes
2
replies
2.1k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 13 months ago by
Will
• 0 • written 7.7 years ago by
metamaden
▴ 10
1
vote
1
reply
413
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 15 months ago by
tcalvo
▴ 90 • written 15 months ago by
megha.hs28
▴ 10
0
votes
0
replies
396
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
16 months ago
Lorenzo
• 0
0
votes
1
reply
556
views
Gene level methylation values
methylation
methylKit
bsseq
updated 20 months ago by
alex.gos90
▴ 10 • written 23 months ago by
ag1805x
▴ 80
1
vote
1
reply
643
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 2.1 years ago by
Robert Ivanek
▴ 730 • written 2.1 years ago by
ltzhou
• 0
2
votes
2
replies
554
views
How to overcome issue linked to loading big R object
minfi
R
methylation
2.1 years ago
Federica
▴ 10
1
vote
5
replies
3.0k
views
minfi - error when reading idat files
minfi
methylation
updated 8 months ago by
Sajad Wani
• 0 • written 5.9 years ago by
stewart999
▴ 10
0
votes
0
replies
658
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
2.4 years ago
epibio
▴ 10
0
votes
1
reply
555
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation
epigenomics
slurm
mpi
methylmix
updated 2.8 years ago by
Kevin Blighe
3.8k • written 2.9 years ago by
parra.sev
▴ 20
0
votes
0
replies
423
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
2.9 years ago
i.s.castanho
• 0
0
votes
1
reply
377
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
3.1 years ago
AishaD
• 0
2
votes
1
reply
656
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
3.1 years ago
Zach Roe
▴ 10
0
votes
0
replies
557
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
3.1 years ago
marcin.bazyliszek
• 0
0
votes
6
replies
983
views
error with champ.load
ChAMP
champ
methylation
updated 22 months ago by
Nidhi
• 0 • written 3.2 years ago by
jkong
• 0
0
votes
1
reply
364
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
3.2 years ago
i.s.castanho
• 0
1
vote
1
reply
598
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 3.3 years ago by
James W. MacDonald
63k • written 3.3 years ago by
whyw6948
• 0
0
votes
4
replies
554
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
3.3 years ago
i.s.brorson
• 0
1
vote
3
replies
915
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
3.4 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
581
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 3.4 years ago by
Yuan Tian
▴ 90 • written 3.4 years ago by
cherlyn.t
• 0
0
votes
0
replies
414
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
3.4 years ago
A
▴ 40
0
votes
1
reply
2.1k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
3.4 years ago
ph.shimaasherif
• 0
2
votes
16
replies
1.6k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 3.4 years ago by
Yuan Tian
▴ 270 • written 3.4 years ago by
Ankit
▴ 20
0
votes
8
replies
629
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
3.4 years ago
sara.blocquiaux
• 0
0
votes
0
replies
437
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
3.4 years ago
luciomora8
• 0
0
votes
1
reply
616
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 3.5 years ago by
Kevin Blighe
3.8k • written 3.5 years ago by
lucasmiranda42
• 0
1
vote
3
replies
667
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 3.5 years ago by
James W. MacDonald
63k • written 3.6 years ago by
yuabrahamliu
• 0
1
vote
3
replies
646
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
3.6 years ago
patriciasolesanchez
• 0
0
votes
1
reply
437
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
3.6 years ago
sorjuelal
• 0
0
votes
2
replies
594
views
Illumina 450K quality controls with meffil
meffil
EWAS
methylation
updated 3.7 years ago by
James W. MacDonald
63k • written 3.7 years ago by
uxue33
• 0
3
votes
5
replies
848
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 3.7 years ago by
James W. MacDonald
63k • written 3.7 years ago by
yoursbassanio
▴ 10
0
votes
0
replies
429
views
DSS for non-CpG site analysis
DSS
methylation
3.7 years ago
CalM
• 0
0
votes
4
replies
1.0k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 4 months ago by
shuo
• 0 • written 3.8 years ago by
enora.fremy
• 0
1
vote
3
replies
1.0k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 3.8 years ago by
tgorri
▴ 10 • written 3.8 years ago by
sara.blocquiaux
• 0
1
vote
6
replies
1.0k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
3.8 years ago
sabrina.mcnew
• 0
1
vote
2
replies
2.6k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 2.1 years ago by
sci_djw
• 0 • written 4.1 years ago by
researcher
• 0
1
vote
4
replies
997
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 4.0 years ago by
keegan
▴ 60 • written 4.0 years ago by
sorjuelal
• 0
0
votes
1
reply
1.4k
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 4.1 years ago by
Yuan Tian
▴ 270 • written 4.1 years ago by
moldach
▴ 20
0
votes
0
replies
940
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks
SummarizedExperiment
TCGAanalyze_DMR
methylation
R
4.2 years ago
gerald.mccollam
• 0
4
votes
4
replies
837
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 4.2 years ago by
Kasper Daniel Hansen
6.5k • written 4.3 years ago by
laurenz.holcik
• 0
0
votes
0
replies
812
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
4.3 years ago
moldach
▴ 20
0
votes
1
reply
639
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 4.4 years ago by
James W. MacDonald
63k • written 4.4 years ago by
lalchungnungabt17
• 0
1
vote
2
replies
1.0k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 4.5 years ago by
Ou, Jianhong
★ 1.3k • written 4.5 years ago by
Adam_M
• 0
2
votes
1
reply
914
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 4.5 years ago by
Yuan Tian
▴ 270 • written 4.5 years ago by
D
• 0
0
votes
0
replies
543
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
4.6 years ago
saripalligautam86
▴ 10
0
votes
2
replies
1.6k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP
Normalization
FunctionalNormalization
methylation
EPIC
4.7 years ago
yuabrahamliu
• 0
1
vote
2
replies
1.6k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 4.7 years ago by
James W. MacDonald
63k • written 4.7 years ago by
moldach
▴ 20
2
votes
8
replies
1.3k
views
edgeR: design matrix for methylation analysis
edger
methylation
updated 4.7 years ago by
Gordon Smyth
47k • written 4.9 years ago by
sgld
• 0
50 results • Page
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Comment: Ensembl plants at annotationHub?
by
Bruno
• 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output
by
betterwound
• 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub?
by
Bruno
• 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable
by
swbarnes2
★ 1.2k
Did you relevel before or after calling DESeq?
Votes
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
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