Showing : Minfi • reset
0
votes
3
replies
1.1k
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 7 months ago by • 0 • written 9 months ago by • 0
1
vote
2
replies
855
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
10 months ago user_bioinfo • 0
4
votes
8
replies
2.0k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
13 months ago • updated 11 months ago xiaofeiwang198266 • 0
1
vote
4
replies
1.1k
views
Handling Epic Array Data
minfi
14 months ago Melisa Tecik • 0
2
votes
2
replies
847
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
14 months ago Rakesh • 0
2
votes
5
replies
1.1k
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
2
replies
1.1k
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 17 months ago by • 0 • written 17 months ago by • 0
4
votes
12
replies
6.1k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 17 months ago by ▴ 230 • written 2.1 years ago by ▴ 20
0
votes
1
reply
802
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 18 months ago by 68k • written 18 months ago by • 0
0
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0
replies
761
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
18 months ago pcibin • 0
0
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2
replies
1.3k
views
Epicv2 conversion fail
minfi
19 months ago • updated 18 months ago Alex • 0
2
votes
4
replies
3.4k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 6 months ago by • 0 • written 20 months ago by • 0
1
vote
4
replies
986
views
minfi::read.metharray.exp
minfiData minfi
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
0
votes
4
replies
1.1k
views
Minfi - estimatecellscount
min minfi
updated 20 months ago by 68k • written 21 months ago by • 0
0
votes
0
replies
810
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
22 months ago Felix • 0
0
votes
1
reply
708
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
7
replies
1.4k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 23 months ago by 68k • written 23 months ago by • 0
1
vote
2
replies
3.3k
views
EPIC array hg38 annotation?
minfi DMRcate
23 months ago mycetes • 0
0
votes
0
replies
1.3k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
2.1 years ago kyj2226 • 0
3
votes
2
replies
1.5k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
2.1 years ago kyj2226 • 0
0
votes
1
reply
945
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
votes
5
replies
1.9k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.3 years ago • updated 2.2 years ago dorota.komar • 0
0
votes
2
replies
1.6k
views
minfi differential methylation analysis errors
minfi
2.3 years ago matthew.sinton • 0
0
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3
replies
1.5k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
0
votes
14
replies
4.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 23 months ago by • 0 • written 2.4 years ago by • 0
1
vote
2
replies
1.5k
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
written 2.4 years ago by ▴ 10
0
votes
3
replies
1.9k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 22 months ago by • 0 • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
votes
0
replies
825
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.8 years ago edward.esiribloom • 0
6
votes
6
replies
11k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 15 months ago by • 0 • written 2.8 years ago by ▴ 50
0
votes
1
reply
1.1k
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
4
replies
2.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
1
vote
3
replies
1.8k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
5
replies
2.3k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.9 years ago by • 0
0
votes
1
reply
1.5k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
2
votes
3
replies
2.2k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 3.0 years ago by ▴ 40 • written 3.0 years ago by • 0
0
votes
1
reply
1.7k
views
minfi read.metharray.sheet error
minfi
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
1
reply
1.9k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
votes
0
replies
1.1k
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
3.4 years ago calen.p.ryan • 0
0
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0
replies
1.1k
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
3.6 years ago runye • 0
0
votes
1
reply
1.5k
views
what is the format of DMPfinder in minfi package
minfi
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
0
votes
3
replies
1.8k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.8 years ago • updated 3.7 years ago ramonfallon ▴ 20
0
votes
2
replies
3.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.7 years ago by • 0 • written 10.3 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.7 years ago octaviompa • 0
0
votes
0
replies
960
views
Minfi package: controlStripPlot colors
minfi
3.9 years ago Rebecca • 0
0
votes
1
reply
1.5k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
0
votes
9
replies
4.4k
views
clarification about bumphunter value output
minfi bumphunter
updated 2.6 years ago by • 0 • written 7.9 years ago by • 0
0
votes
1
reply
1.4k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 4.3 years ago by ▴ 780 • written 4.3 years ago by • 0
0
votes
0
replies
1.3k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.4 years ago ponche_de_kiwi • 0
281 results • Page 1 of 6
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Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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