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Showing :
methylation
•
reset
1
vote
2
replies
355
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 11 days ago
Kim
• 0
0
votes
1
reply
172
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
ja569116
• 0
1
vote
8
replies
565
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
272
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 6 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 9 months ago by
mike
• 0 • written 4.1 years ago by
jkong
• 0
0
votes
2
replies
771
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
585
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
661
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
788
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
738
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
875
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 6.9 years ago by
stewart999
▴ 10
0
votes
0
replies
974
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
871
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
754
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
647
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
1.0k
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
4.1 years ago
Zach Roe
▴ 10
0
votes
0
replies
888
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
4.1 years ago
marcin.bazyliszek
• 0
0
votes
1
reply
613
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
954
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
921
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
4.3 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
827
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
708
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
4.4 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 4.4 years ago by
Yuan Tian
▴ 290 • written 4.4 years ago by
Ankit
▴ 20
0
votes
8
replies
1.0k
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
4.4 years ago
sara.blocquiaux
• 0
0
votes
0
replies
681
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
4.4 years ago
luciomora8
• 0
0
votes
1
reply
985
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
1.1k
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
702
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
4.6 years ago
sorjuelal
• 0
0
votes
2
replies
866
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
735
views
DSS for non-CpG site analysis
DSS
methylation
4.7 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 16 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
3.7k
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
2.1k
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 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
5.3 years ago • updated 5.2 years ago
moldach
▴ 20
0
votes
1
reply
932
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
▴ 290 • written 5.5 years ago by
D
▴ 10
50 results • Page
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Comment: error running enricher from clusterprofiler
by
Yael
• 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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