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methylation
•
reset
0
votes
5
replies
2.2k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
written 8.7 years ago by
aagata.szymanek
• 0
0
votes
13
replies
1.6k
views
When doing differential methylation using the sesame package, seems to only go one way
methylation
sesame
methylationArrayAnalysis
updated 7 months ago by
zhouwanding
▴ 20 • written 7 months ago by
ramiro.barrantes
▴ 10
1
vote
2
replies
842
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
7 months ago
ramiro.barrantes
▴ 10
1
vote
3
replies
2.5k
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 6 months ago by
rania.alanany
• 0 • written 12 months ago by
Kim
• 0
0
votes
1
reply
708
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
ja569116
• 0
1
vote
8
replies
1.2k
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 15 months ago by
Gordon Smyth
52k • written 15 months ago by
sat
• 0
0
votes
0
replies
930
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
16 months ago
kyj2226
• 0
1
vote
3
replies
2.3k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 17 months ago by
Robert Ivanek
▴ 750 • written 4.0 years ago by
ltzhou
• 0
0
votes
7
replies
2.5k
views
error with champ.load
ChAMP
champ
methylation
updated 20 months ago by
mike
• 0 • written 5.0 years ago by
jkong
• 0
0
votes
2
replies
1.2k
views
error in champ.SVD
svd
methylation
champ
updated 2.0 years ago by
shepherl
4.1k • written 2.0 years ago by
Giulia
• 0
1
vote
0
replies
855
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
2.8 years ago
hlee
▴ 10
2
votes
1
reply
939
views
Limma model orientation
limma
methylation
MethylationArray
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
fluentin44
• 0
0
votes
2
replies
3.4k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 3.0 years ago by
Will
• 0 • written 9.6 years ago by
metamaden
▴ 10
1
vote
1
reply
1.1k
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 3.1 years ago by
tcalvo
▴ 100 • written 3.1 years ago by
megha.hs28
▴ 10
0
votes
0
replies
976
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
3.2 years ago
Lorenzo
• 0
0
votes
1
reply
2.1k
views
Gene level methylation values
methylation
methylKit
bsseq
updated 3.5 years ago by
alex.gos90
▴ 10 • written 3.8 years ago by
Arindam
▴ 80
2
votes
2
replies
1.2k
views
How to overcome issue linked to loading big R object
minfi
R
methylation
4.0 years ago
Federica
▴ 10
1
vote
5
replies
5.2k
views
minfi - error when reading idat files
minfi
methylation
updated 2.6 years ago by
Sajad Wani
• 0 • written 7.8 years ago by
stewart999
▴ 10
0
votes
0
replies
1.2k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
4.3 years ago
epibio
▴ 10
0
votes
1
reply
1.1k
views
how to paralelize this R script in a HPC cluster using Slurm Workload Manager?
methylation
epigenomics
slurm
mpi
methylmix
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
parra.sev
▴ 20
0
votes
0
replies
984
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.8 years ago
i.s.castanho
• 0
0
votes
1
reply
897
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.9 years ago
AishaD
• 0
2
votes
1
reply
1.3k
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
5.0 years ago
Zach Roe
▴ 10
0
votes
0
replies
1.2k
views
Deconvolution methods from WGBS data (methylation)
methylCC
deconvolution
methylation
dmrseq
serum
5.0 years ago
marcin.bazyliszek
• 0
0
votes
1
reply
842
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
5.1 years ago
i.s.castanho
• 0
1
vote
1
reply
1.3k
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
whyw6948
• 0
0
votes
4
replies
1.3k
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
5.2 years ago
i.s.brorson
• 0
1
vote
3
replies
1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.2 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
1.1k
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 5.3 years ago by
Yuan Tian
▴ 90 • written 5.3 years ago by
cherlyn.t
• 0
0
votes
0
replies
962
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
5.3 years ago
A
▴ 60
0
votes
1
reply
3.4k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
5.3 years ago
ph.shimaasherif
• 0
2
votes
16
replies
3.8k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 5.3 years ago by
Yuan Tian
▴ 290 • written 5.3 years ago by
Ankit
▴ 20
0
votes
8
replies
1.4k
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
5.3 years ago
sara.blocquiaux
• 0
0
votes
0
replies
903
views
Methylmix results are a bit different from beta values results
cancer
methylmix
methylation
betavalues
DMvalues
5.3 years ago
luciomora8
• 0
0
votes
1
reply
1.4k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
lucasmiranda42
• 0
1
vote
3
replies
1.5k
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
yuabrahamliu
• 0
1
vote
3
replies
1.5k
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
5.5 years ago
patriciasolesanchez
• 0
0
votes
1
reply
969
views
Suggestion dmrseq: generate Error when the adjustCovariate(s) generates a design that is not full rank
dmrseq
methylation
5.5 years ago
sorjuelal
• 0
0
votes
2
replies
1.1k
views
Illumina 450K quality controls with meffil
meffil
EWAS
methylation
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
uxue33
• 0
3
votes
5
replies
1.8k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 5.5 years ago by
James W. MacDonald
68k • written 5.6 years ago by
yoursbassanio
▴ 10
0
votes
0
replies
992
views
DSS for non-CpG site analysis
DSS
methylation
5.6 years ago
CalM
• 0
0
votes
4
replies
2.2k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 2.3 years ago by
shuo
• 0 • written 5.7 years ago by
enora.fremy
• 0
1
vote
3
replies
2.0k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 5.7 years ago by
tgorri
▴ 10 • written 5.7 years ago by
sara.blocquiaux
• 0
1
vote
6
replies
2.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
5.7 years ago
sabrina.mcnew
• 0
1
vote
2
replies
4.6k
views
minfi error in read.metharray
minfi
methylation
idat
samplesheet
updated 4.0 years ago by
sci_djw
• 0 • written 6.0 years ago by
researcher
• 0
1
vote
4
replies
2.1k
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 5.9 years ago by
keegan
▴ 60 • written 5.9 years ago by
sorjuelal
• 0
0
votes
2
replies
2.6k
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 17 months ago by
peter.brederlo
• 0 • written 6.0 years ago by
moldach
▴ 20
0
votes
0
replies
1.5k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks
SummarizedExperiment
TCGAanalyze_DMR
methylation
R
6.1 years ago
gerald.mccollam
• 0
4
votes
4
replies
1.7k
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 6.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.1 years ago by
laurenz.holcik
• 0
0
votes
0
replies
1.4k
views
Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation
ENmix
BMIQ
wateRmelon
6.2 years ago
moldach
▴ 20
50 results • Page
1 of 1
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Comment: Differing results with DESeq2
by
JKim
• 0
I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for gene expressio…
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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