Showing : Minfi • reset
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120
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 20 hours ago by 68k • written 21 hours ago by • 0
1
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2
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556
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
4 weeks 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 5 weeks ago xiaofeiwang198266 • 0
1
vote
4
replies
585
views
Handling Epic Array Data
minfi
4 months ago Melisa Tecik • 0
2
votes
2
replies
479
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preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
4 months ago Rakesh • 0
2
votes
5
replies
719
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 5 months ago by 68k • written 5 months ago by • 0
0
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2
replies
681
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 7 months ago by • 0 • written 7 months ago by • 0
3
votes
12
replies
4.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 8 months ago by ▴ 230 • written 16 months ago by ▴ 10
0
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1
reply
557
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 8 months ago by 68k • written 8 months ago by • 0
0
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0
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499
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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
825
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 12 weeks ago by • 0 • written 10 months ago by • 0
1
vote
4
replies
634
views
minfi::read.metharray.exp
minfiData minfi
updated 11 months ago by ▴ 780 • written 11 months ago by • 0
0
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4
replies
818
views
Minfi - estimatecellscount
min minfi
updated 11 months ago by 68k • written 12 months ago by • 0
0
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0
replies
638
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
495
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
7
replies
1.1k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 13 months ago by 68k • written 13 months ago by • 0
1
vote
2
replies
2.3k
views
EPIC array hg38 annotation?
minfi DMRcate
13 months ago mycetes • 0
0
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0
replies
863
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
733
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 16 months ago by ▴ 780 • written 16 months ago by • 0
0
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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
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2
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1.3k
views
minfi differential methylation analysis errors
minfi
17 months ago matthew.sinton • 0
0
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3
replies
1.2k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
votes
14
replies
3.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 14 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
776
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 19 months ago by 68k • written 19 months ago by • 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 ▴ 780 • written 22 months ago by ▴ 10
0
votes
2
replies
889
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 12 months ago by • 0 • written 22 months ago by • 0
0
votes
1
reply
867
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 24 months ago by 52k • written 24 months ago by • 0
0
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0
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646
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 • 0 • written 2.0 years ago by ▴ 50
0
votes
1
reply
933
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.0 years ago by 68k • written 2.0 years ago by • 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 68k • written 2.1 years ago by • 0
1
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3
replies
1.4k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.0 years ago by 68k • written 2.1 years ago by • 0
0
votes
5
replies
1.9k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.1 years ago by • 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 68k • written 2.1 years ago by • 0
2
votes
3
replies
1.7k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.2 years ago by ▴ 40 • written 2.2 years ago by • 0
0
votes
1
reply
1.5k
views
minfi read.metharray.sheet error
minfi
updated 2.3 years ago by 68k • written 2.3 years ago by • 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 68k • written 2.6 years ago by • 0
0
votes
0
replies
821
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
960
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.8 years ago runye • 0
0
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1
reply
1.3k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
3
replies
1.6k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.0 years ago • updated 2.9 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 • 0 • written 9.5 years ago by ▴ 10
0
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0
replies
1.3k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.9 years ago octaviompa • 0
0
votes
0
replies
837
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 68k • written 3.1 years ago by • 0
0
votes
9
replies
3.9k
views
clarification about bumphunter value output
minfi bumphunter
updated 22 months ago by • 0 • written 7.1 years ago by • 0
0
votes
1
reply
1.2k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
0
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0
replies
1.1k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.6 years ago ponche_de_kiwi • 0
50 results • Page 1 of 1
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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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