Showing : Minfi • reset
0
votes
3
replies
934
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 4 months ago by • 0 • written 6 months ago by • 0
1
vote
2
replies
759
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
7 months ago user_bioinfo • 0
4
votes
8
replies
1.7k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
10 months ago • updated 7 months ago xiaofeiwang198266 • 0
1
vote
4
replies
900
views
Handling Epic Array Data
minfi
10 months ago Melisa Tecik • 0
2
votes
2
replies
738
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
10 months ago Rakesh • 0
2
votes
5
replies
971
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
2
replies
968
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 13 months ago by • 0 • written 14 months ago by • 0
4
votes
12
replies
5.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 14 months ago by ▴ 230 • written 22 months ago by ▴ 20
0
votes
1
reply
719
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
0
replies
667
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
15 months ago pcibin • 0
0
votes
2
replies
1.1k
views
Epicv2 conversion fail
minfi
16 months ago • updated 15 months ago Alex • 0
2
votes
4
replies
3.1k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 3 months ago by • 0 • written 17 months ago by • 0
1
vote
4
replies
853
views
minfi::read.metharray.exp
minfiData minfi
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
votes
4
replies
990
views
Minfi - estimatecellscount
min minfi
updated 17 months ago by 68k • written 18 months ago by • 0
0
votes
0
replies
754
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
19 months ago Felix • 0
0
votes
1
reply
636
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
7
replies
1.3k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
2
replies
2.9k
views
EPIC array hg38 annotation?
minfi DMRcate
20 months ago mycetes • 0
0
votes
0
replies
1.1k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
22 months ago kyj2226 • 0
3
votes
2
replies
1.3k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
22 months ago kyj2226 • 0
0
votes
1
reply
858
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 22 months ago by ▴ 780 • written 23 months ago by • 0
0
votes
5
replies
1.8k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.0 years ago • updated 24 months ago dorota.komar • 0
0
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2
replies
1.5k
views
minfi differential methylation analysis errors
minfi
2.0 years ago • updated 24 months ago matthew.sinton • 0
0
votes
3
replies
1.4k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
0
votes
14
replies
4.4k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 20 months ago by • 0 • written 2.1 years ago by • 0
1
vote
2
replies
1.4k
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 3 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by ▴ 10
0
votes
2
replies
1.1k
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 18 months ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
1.0k
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
votes
0
replies
760
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.6 years ago edward.esiribloom • 0
6
votes
6
replies
10k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 12 months ago by • 0 • written 2.6 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 2.6 years ago by 68k • written 2.6 years ago by • 0
0
votes
4
replies
1.9k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
1
vote
3
replies
1.6k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
votes
5
replies
2.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.6 years ago by • 0
0
votes
1
reply
1.4k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
2
votes
3
replies
2.0k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
0
votes
1
reply
1.6k
views
minfi read.metharray.sheet error
minfi
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
1
reply
1.7k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
943
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
3.2 years ago calen.p.ryan • 0
0
votes
0
replies
1.1k
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
3.3 years ago runye • 0
0
votes
1
reply
1.5k
views
what is the format of DMPfinder in minfi package
minfi
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
3
replies
1.7k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.5 years ago • updated 3.4 years ago ramonfallon ▴ 20
0
votes
2
replies
3.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.5 years ago by • 0 • written 10.0 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.5 years ago octaviompa • 0
0
votes
0
replies
916
views
Minfi package: controlStripPlot colors
minfi
3.6 years ago Rebecca • 0
0
votes
1
reply
1.4k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
9
replies
4.2k
views
clarification about bumphunter value output
minfi bumphunter
updated 2.4 years ago by • 0 • written 7.6 years ago by • 0
0
votes
1
reply
1.4k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
0
votes
0
replies
1.2k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.2 years ago ponche_de_kiwi • 0
281 results • Page 1 of 6
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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