Showing : minfi • reset
0
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3
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1.3k
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Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 8 months ago by • 0 • written 10 months ago by • 0
1
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2
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876
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
11 months ago user_bioinfo • 0
4
votes
8
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2.2k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
14 months ago • updated 12 months ago xiaofeiwang198266 • 0
1
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4
replies
1.1k
views
Handling Epic Array Data
minfi
15 months ago Melisa Tecik • 0
2
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2
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899
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preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
15 months ago Rakesh • 0
2
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5
replies
1.2k
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 16 months ago by 68k • written 16 months ago by • 0
0
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2
replies
1.1k
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 18 months ago by • 0 • written 18 months ago by • 0
4
votes
12
replies
6.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 18 months ago by ▴ 230 • written 2.2 years ago by ▴ 20
0
votes
1
reply
840
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 19 months ago by 68k • written 19 months ago by • 0
0
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0
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817
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Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
19 months ago pcibin • 0
0
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2
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1.4k
views
Epicv2 conversion fail
minfi
20 months ago • updated 19 months ago Alex • 0
2
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4
replies
3.6k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 7 months ago by • 0 • written 21 months ago by • 0
1
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4
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1.0k
views
minfi::read.metharray.exp
minfiData minfi
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
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4
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1.2k
views
Minfi - estimatecellscount
min minfi
updated 21 months ago by 68k • written 22 months ago by • 0
0
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0
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837
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
23 months ago Felix • 0
0
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1
reply
720
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 23 months ago by 68k • written 23 months ago by • 0
0
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7
replies
1.4k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
1
vote
2
replies
3.7k
views
EPIC array hg38 annotation?
minfi DMRcate
2.0 years ago mycetes • 0
0
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0
replies
1.4k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
2.2 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
2.2 years ago kyj2226 • 0
0
votes
1
reply
965
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
0
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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 dorota.komar • 0
0
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2
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1.7k
views
minfi differential methylation analysis errors
minfi
2.3 years ago matthew.sinton • 0
0
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3
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1.6k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
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14
replies
4.9k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 2.0 years ago by • 0 • written 2.5 years ago by • 0
1
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2
replies
1.6k
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
written 2.5 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 2.8 years ago by ▴ 780 • written 2.8 years ago by ▴ 10
0
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2
replies
1.2k
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 23 months ago by • 0 • written 2.8 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 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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0
replies
846
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.9 years ago edward.esiribloom • 0
6
votes
6
replies
11k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 16 months ago by • 0 • written 2.9 years ago by ▴ 50
0
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1
reply
1.2k
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
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4
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2.1k
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
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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
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5
replies
2.4k
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 3.0 years ago by 68k • written 3.0 years ago by • 0
2
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3
replies
2.3k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 3.1 years ago by ▴ 40 • written 3.1 years ago by • 0
0
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1
reply
1.7k
views
minfi read.metharray.sheet error
minfi
updated 3.2 years ago by 68k • written 3.2 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 3.5 years ago by 68k • written 3.5 years ago by • 0
0
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0
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1.1k
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
3.5 years ago calen.p.ryan • 0
0
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0
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1.1k
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
3.7 years ago runye • 0
0
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1
reply
1.6k
views
what is the format of DMPfinder in minfi package
minfi
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
0
votes
3
replies
1.9k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.9 years ago • updated 3.7 years ago ramonfallon ▴ 20
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2
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3.8k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.8 years ago by • 0 • written 10.4 years ago by ▴ 10
0
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0
replies
1.7k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.8 years ago octaviompa • 0
0
votes
0
replies
970
views
Minfi package: controlStripPlot colors
minfi
4.0 years ago Rebecca • 0
0
votes
1
reply
1.6k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
9
replies
4.4k
views
clarification about bumphunter value output
minfi bumphunter
updated 2.7 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 4.4 years ago by ▴ 780 • written 4.4 years ago by • 0
0
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0
replies
1.4k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.5 years ago ponche_de_kiwi • 0
281 results • Page 1 of 6
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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