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minfi
•
reset
1
vote
2
replies
545
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
29 days ago
user_bioinfo
• 0
4
votes
8
replies
1.2k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate
minfi
3 months ago • updated 4 weeks ago
xiaofeiwang198266
• 0
1
vote
4
replies
570
views
Handling Epic Array Data
minfi
4 months ago
Melisa Tecik
• 0
2
votes
2
replies
468
views
preprocessIllumina error with EPICv2 array
minfi
EPICv2manifest
4 months ago
Rakesh
• 0
2
votes
5
replies
711
views
dmpFinder for other objects
methylset
minfi
dmpFinder
betaHMM
beta
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
neyousha
• 0
0
votes
2
replies
671
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 7 months ago by
nrenke
• 0 • written 7 months ago by
Lucie
• 0
3
votes
12
replies
4.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 7 months ago by
Tim Peters
▴ 230 • written 16 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
550
views
minfi - bumphunter value problem
bumphunter
minfiData
minfi
bumphun
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
kumakeren16
• 0
0
votes
0
replies
493
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
8 months ago
pcibin
• 0
0
votes
2
replies
812
views
Epicv2 conversion fail
minfi
9 months ago • updated 8 months ago
Alex
• 0
2
votes
3
replies
1.7k
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 11 weeks ago by
macdonaldfrench7286566
• 0 • written 10 months ago by
e1271094
• 0
1
vote
4
replies
626
views
minfi::read.metharray.exp
minfiData
minfi
updated 11 months ago by
Basti
▴ 780 • written 11 months ago by
clacarion
• 0
0
votes
4
replies
806
views
Minfi - estimatecellscount
min
minfi
updated 10 months ago by
James W. MacDonald
68k • written 11 months ago by
clacarion
• 0
0
votes
0
replies
633
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
12 months ago
Felix
• 0
0
votes
1
reply
491
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
sharangiiv
• 0
0
votes
7
replies
1.1k
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
sharangiiv
• 0
1
vote
2
replies
2.3k
views
EPIC array hg38 annotation?
minfi
DMRcate
13 months ago
mycetes
• 0
0
votes
0
replies
852
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
15 months ago
kyj2226
• 0
3
votes
2
replies
1.1k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
15 months ago
kyj2226
• 0
0
votes
1
reply
730
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 16 months ago by
Basti
▴ 780 • written 16 months ago by
Ana
• 0
0
votes
5
replies
1.5k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
17 months ago
dorota.komar
• 0
0
votes
2
replies
1.3k
views
minfi differential methylation analysis errors
minfi
17 months ago
matthew.sinton
• 0
0
votes
3
replies
1.1k
views
minfi bumphunter - probe IDs
minfi
bumphunter
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
dorota.komar
• 0
0
votes
14
replies
3.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 13 months ago by
nguyen
• 0 • written 18 months ago by
Deepa
• 0
0
votes
1
reply
768
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC
minfi
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
phelankj
• 0
0
votes
3
replies
1.5k
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 22 months ago by
Basti
▴ 780 • written 22 months ago by
Jitendra
▴ 10
0
votes
2
replies
887
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 12 months ago by
CHEN
• 0 • written 22 months ago by
Saanchi
• 0
0
votes
1
reply
864
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 23 months ago by
Gordon Smyth
52k • written 24 months ago by
Grace
• 0
0
votes
0
replies
643
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
2.0 years ago
edward.esiribloom
• 0
6
votes
6
replies
9.3k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 5 months ago by
wl_xxz
• 0 • written 2.0 years ago by
luca.s
▴ 50
0
votes
1
reply
929
views
specifying comparison of interest in the minfi Bumhunter function
limma
bumphunter
methylationArrayAnalysis
minfi
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
edward.esiribloom
• 0
0
votes
4
replies
1.6k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Grace
• 0
1
vote
3
replies
1.4k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
alyena
• 0
0
votes
5
replies
1.9k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 2.0 years ago by
Grace
• 0
0
votes
1
reply
1.2k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic
read.metharray.sheet
list.files
minfi
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Diogenesis
• 0
2
votes
3
replies
1.6k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.2 years ago by
belinda.phipson
▴ 40 • written 2.2 years ago by
Lukas
• 0
0
votes
1
reply
1.5k
views
minfi read.metharray.sheet error
minfi
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
jasmine_chappell
• 0
0
votes
1
reply
1.5k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile
noob
Normalization
minfi
minfiDataEPIC
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
mikat
• 0
0
votes
0
replies
818
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
2.6 years ago
calen.p.ryan
• 0
0
votes
0
replies
958
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter
minfi
genomi
2.8 years ago
runye
• 0
0
votes
1
reply
1.3k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
Fateme
• 0
0
votes
3
replies
1.6k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
3.0 years ago • updated 2.8 years ago
ramonfallon
▴ 20
0
votes
2
replies
3.3k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 2.9 years ago by
Will
• 0 • written 9.5 years ago by
metamaden
▴ 10
0
votes
0
replies
1.3k
views
Annotation Illumina Infinium Mouse Methylation
Illumina
minfi
IlluminaHumanMethylationEPICmanifest
2.9 years ago
octaviompa
• 0
0
votes
0
replies
835
views
Minfi package: controlStripPlot colors
minfi
3.1 years ago
Rebecca
• 0
0
votes
1
reply
1.2k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
failingprobes
detectionP
minfi
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Lilly
• 0
0
votes
9
replies
3.9k
views
clarification about bumphunter value output
minfi
bumphunter
updated 22 months ago by
Jennifer Dehner
• 0 • written 7.0 years ago by
src3
• 0
0
votes
1
reply
1.2k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC
#SexPrediction
minfi
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
nucasa
• 0
0
votes
0
replies
1.1k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi
minfiData
MethylationArrayData
3.6 years ago
ponche_de_kiwi
• 0
3
votes
6
replies
2.3k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
Sophie Marion de Proce
• 0
50 results • Page
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Recent ...
Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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