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methylation
•
reset
2
votes
16
replies
2.5k
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
▴ 270 • written 4.3 years ago by
Ankit
▴ 20
3
votes
15
replies
4.3k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.0 years ago
rasii
• 0
6
votes
14
replies
4.7k
views
How to correctly import Bismark coverage files into bsseq?
bsseq
bismark
methylation
8.4 years ago
enricoferrero
▴ 660
0
votes
13
replies
2.4k
views
handling missing data (NA) for methylaion analysis in Limma
limma
missing data
methylation
normalization
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mheydarpour
▴ 10
14
votes
12
replies
9.2k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
CPR
▴ 30
2
votes
11
replies
9.1k
views
Minfi error in reading Basename column
methylation
minfi
updated 7.5 years ago by
SplittingInfinity
▴ 60 • written 8.6 years ago by
parap
• 0
5
votes
9
replies
1.7k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
c.bettencourt
• 0
1
vote
9
replies
2.6k
views
bumphunter beta values
methylation
minfi
bumphunter
updated 8.0 years ago by
James W. MacDonald
65k • written 8.0 years ago by
igor
▴ 40
1
vote
9
replies
3.6k
views
strange results from differential methylation analysis using limma
limma
methylation
methyanalysis
IMA
updated 23 months ago by
Sean Davis
21k • written 7.1 years ago by
RC
• 0
2
votes
8
replies
1.9k
views
edgeR: design matrix for methylation analysis
edger
methylation
updated 5.6 years ago by
Gordon Smyth
50k • written 5.8 years ago by
sgld
• 0
4
votes
8
replies
3.7k
views
minfi MethylationEPIC errors
minfi
methylation
IlluminaHumanMethylationEPICmanifest
IlluminaHumanMethylationEPICanno.ilmn10b.hg19
updated 8.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.1 years ago by
igor
▴ 40
0
votes
8
replies
994
views
DeSeq2: error in design individuals nested within groups
deseq2
methylation
4.3 years ago
sara.blocquiaux
• 0
1
vote
8
replies
508
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
sat
• 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
7
replies
1.8k
views
error with champ.load
ChAMP
champ
methylation
updated 8 months ago by
mike
• 0 • written 4.0 years ago by
jkong
• 0
0
votes
7
replies
2.9k
views
Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
minfi
methylation
dmpfinder
limma
updated 6.9 years ago by
vulegom
• 0 • written 7.6 years ago by
mcall
▴ 20
0
votes
6
replies
3.0k
views
difference in detection p-values from Minfi vs. GenomeStudio
minfi
genomestudio
methylation
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
brhead
▴ 40
0
votes
6
replies
1.4k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
6.2 years ago • updated 6.1 years ago
dusan.petrovic
• 0
1
vote
6
replies
1.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.6 years ago
sabrina.mcnew
• 0
1
vote
5
replies
2.8k
views
About methylation data processing
methylation
updated 8.2 years ago by
Peter Hickey
▴ 710 • written 8.2 years ago by
Asma rabe
▴ 290
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
yoursbassanio
▴ 10
1
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi
methylation
updated 19 months ago by
Sajad Wani
• 0 • written 6.8 years ago by
stewart999
▴ 10
0
votes
5
replies
2.2k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon
methylation
EPIC
normalization
7.3 years ago
Wade Davis
▴ 60
1
vote
5
replies
1.3k
views
Understanding methyAnalysis Results
methyAnalysis
methyanalysis
methylation
illuminahumanmethylation450k.db
updated 9.1 years ago by
Pan Du
▴ 80 • written 9.1 years ago by
andrew.j.skelton73
▴ 370
0
votes
4
replies
1.6k
views
minfi sample limit
minfi
illumina
illimina 450k methylation
methylation
updated 8.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.1 years ago by
igor
▴ 40
1
vote
4
replies
1.4k
views
M3D package in Bioconductor 3.4
bioconductor
methylation
updated 7.4 years ago by
Dimitris Polychronopoulos
▴ 80 • written 7.4 years ago by
francescacairoli
• 0
0
votes
4
replies
1.1k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation
minfi
ChAMP
updated 5.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.6 years ago by
elgomez
• 0
0
votes
4
replies
2.1k
views
Error with Minfi while using read.metharray.exp() and read.metharray function
minfi
illumina450k
methylation
7.4 years ago
hrishi27n
▴ 20
0
votes
4
replies
1.5k
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 4.6 years ago by
enora.fremy
• 0
0
votes
4
replies
1.6k
views
minfi "mapToGenome" dimension error
methylation
epic microarray
minfi
methylationepic
7.1 years ago
nhejazi
• 0
0
votes
4
replies
1.9k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
updated 7.6 years ago by
b2cemaillist
• 0 • written 7.7 years ago by
aagata.szymanek
• 0
1
vote
4
replies
1.5k
views
dmrseq error: promise already under evaluation??
dmrseq
Methylation
updated 4.8 years ago by
keegan
▴ 60 • written 4.8 years ago by
sorjuelal
• 0
4
votes
4
replies
3.0k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation
dmr analysis
bumphunter
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
chelsey.ju
• 0
0
votes
4
replies
896
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
4.2 years ago
i.s.brorson
• 0
4
votes
4
replies
1.2k
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 5.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.1 years ago by
laurenz.holcik
• 0
0
votes
3
replies
1.6k
views
Minfi error when using force=TRUE in read.metharray
minfi
methylation
epic
5.7 years ago
jbar3141
• 0
0
votes
3
replies
1.7k
views
SVA package for RRBS - bisulfite methylation data
rrbs
batch effect
methylation
sva
updated 7.5 years ago by
dashbrook1
• 0 • written 8.7 years ago by
GFM
▴ 20
1
vote
3
replies
1.3k
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
1
vote
3
replies
1.5k
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
yoursbassanio
▴ 10
1
vote
3
replies
1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation
limma
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
yuabrahamliu
• 0
1
vote
3
replies
1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer
methylation
lolliplot
4.4 years ago
patriciasolesanchez
• 0
1
vote
3
replies
1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.2 years ago
erwin.tomasich
▴ 10
0
votes
3
replies
1.3k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 7.3 years ago by
Katja Hebestreit
▴ 130 • written 7.3 years ago by
jjalmagro
• 0
2
votes
3
replies
2.0k
views
"Seems your IDAT file not from one Array"
EPIC
methylation
ChAMP
updated 6.0 years ago by
yura.grabovska
▴ 30 • written 6.0 years ago by
david.ch
• 0
1
vote
3
replies
1.4k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
6.8 years ago
ezrabekele17
• 0
1
vote
3
replies
1.4k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon
minfi
methylation
pfilter
preprocessNoob
updated 4.6 years ago by
tgorri
▴ 10 • written 4.6 years ago by
sara.blocquiaux
• 0
2
votes
2
replies
1.4k
views
dmrseq: cannot adjust for a covariate
dmrseq
dmr
dmrs
bisulfite
methylation
updated 6.2 years ago by
keegan
▴ 60 • written 6.2 years ago by
l.kremer
• 0
0
votes
2
replies
1.8k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 8.5 years ago by
Sean Davis
21k • written 8.5 years ago by
maria.keays
• 0
0
votes
2
replies
2.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 24 months ago by
Will
• 0 • written 8.5 years ago by
metamaden
▴ 10
0
votes
2
replies
2.0k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
7.4 years ago
hrishi27n
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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