Showing : Minfi • reset
0
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8
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638
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how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
updated 8 hours ago by • 0 • written 8 weeks ago by • 0
1
vote
4
replies
467
views
Handling Epic Array Data
minfi
10 weeks ago • updated 9 weeks ago Melisa Tecik • 0
2
votes
2
replies
374
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preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
10 weeks ago Rakesh • 0
2
votes
5
replies
576
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 3 months ago by 67k • written 3 months ago by • 0
0
votes
2
replies
568
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 5 months ago by • 0 • written 5 months ago by • 0
3
votes
12
replies
4.0k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 6 months ago by ▴ 200 • written 14 months ago by ▴ 10
0
votes
1
reply
480
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
0
replies
419
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
7 months ago pcibin • 0
0
votes
2
replies
710
views
Epicv2 conversion fail
minfi
7 months ago Alex • 0
2
votes
3
replies
1.5k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 28 days ago by • 0 • written 8 months ago by • 0
1
vote
4
replies
558
views
minfi::read.metharray.exp
minfiData minfi
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
0
votes
4
replies
705
views
Minfi - estimatecellscount
min minfi
updated 9 months ago by 67k • written 10 months ago by • 0
0
votes
0
replies
565
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
10 months ago Felix • 0
0
votes
1
reply
440
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 11 months ago by 67k • written 11 months ago by • 0
0
votes
7
replies
993
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 11 months ago by 67k • written 11 months ago by • 0
1
vote
2
replies
2.0k
views
EPIC array hg38 annotation?
minfi DMRcate
11 months ago mycetes • 0
0
votes
0
replies
713
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
13 months ago kyj2226 • 0
3
votes
2
replies
958
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
13 months ago kyj2226 • 0
0
votes
1
reply
684
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
5
replies
1.4k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
15 months ago dorota.komar • 0
0
votes
2
replies
1.2k
views
minfi differential methylation analysis errors
minfi
15 months ago matthew.sinton • 0
0
votes
3
replies
1.1k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 16 months ago by ▴ 780 • written 16 months ago by • 0
0
votes
14
replies
3.5k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 12 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
693
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 17 months ago by 67k • written 17 months ago by • 0
0
votes
3
replies
1.4k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 20 months ago by ▴ 780 • written 20 months ago by ▴ 10
0
votes
2
replies
840
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 10 months ago by • 0 • written 20 months ago by • 0
0
votes
1
reply
776
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 22 months ago by 52k • written 22 months ago by • 0
0
votes
0
replies
607
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
22 months ago edward.esiribloom • 0
6
votes
6
replies
8.8k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 3 months ago by • 0 • written 22 months ago by ▴ 50
0
votes
1
reply
891
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 22 months ago by 67k • written 22 months ago by • 0
0
votes
4
replies
1.5k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 23 months ago by 67k • written 23 months ago by • 0
1
vote
3
replies
1.3k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 23 months ago by 67k • written 23 months ago by • 0
0
votes
5
replies
1.8k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 23 months ago by • 0
0
votes
1
reply
1.1k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 23 months ago by 67k • written 23 months ago by • 0
2
votes
3
replies
1.5k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
0
votes
1
reply
1.4k
views
minfi read.metharray.sheet error
minfi
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
0
votes
1
reply
1.4k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
0
votes
0
replies
760
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.5 years ago calen.p.ryan • 0
0
votes
0
replies
927
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.6 years ago runye • 0
0
votes
1
reply
1.3k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
0
votes
3
replies
1.5k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.8 years ago • updated 2.7 years ago ramonfallon ▴ 20
0
votes
2
replies
3.2k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.8 years ago by • 0 • written 9.3 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.8 years ago octaviompa • 0
0
votes
0
replies
809
views
Minfi package: controlStripPlot colors
minfi
2.9 years ago Rebecca • 0
0
votes
1
reply
1.1k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
0
votes
9
replies
3.7k
views
clarification about bumphunter value output
minfi bumphunter
updated 20 months ago by • 0 • written 6.9 years ago by • 0
0
votes
1
reply
1.2k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
votes
0
replies
1.0k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.5 years ago ponche_de_kiwi • 0
3
votes
6
replies
2.2k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
0
votes
0
replies
966
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3.7 years ago kyleyxw • 0
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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