Showing : Minfi • reset
0
votes
2
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498
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
1
vote
2
replies
599
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
10 weeks ago user_bioinfo • 0
4
votes
8
replies
1.3k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
5 months ago • updated 10 weeks ago xiaofeiwang198266 • 0
1
vote
4
replies
670
views
Handling Epic Array Data
minfi
5 months ago Melisa Tecik • 0
2
votes
2
replies
554
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
5 months ago Rakesh • 0
2
votes
5
replies
785
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 6 months ago by 68k • written 6 months ago by • 0
0
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2
replies
772
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 8 months ago by • 0 • written 8 months ago by • 0
4
votes
12
replies
5.0k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 9 months ago by ▴ 230 • written 17 months ago by ▴ 20
0
votes
1
reply
599
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 9 months ago by 68k • written 9 months ago by • 0
0
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0
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535
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Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
10 months ago pcibin • 0
0
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2
replies
902
views
Epicv2 conversion fail
minfi
10 months ago Alex • 0
2
votes
3
replies
1.9k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 4 months ago by • 0 • written 12 months ago by • 0
1
vote
4
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672
views
minfi::read.metharray.exp
minfiData minfi
updated 12 months ago by ▴ 780 • written 12 months ago by • 0
0
votes
4
replies
869
views
Minfi - estimatecellscount
min minfi
updated 12 months ago by 68k • written 13 months ago by • 0
0
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0
replies
662
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
14 months ago Felix • 0
0
votes
1
reply
514
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
7
replies
1.1k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
2
replies
2.5k
views
EPIC array hg38 annotation?
minfi DMRcate
14 months ago mycetes • 0
0
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0
replies
949
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
16 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
16 months ago kyj2226 • 0
0
votes
1
reply
756
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
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5
replies
1.6k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
18 months ago dorota.komar • 0
0
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2
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1.3k
views
minfi differential methylation analysis errors
minfi
18 months ago matthew.sinton • 0
0
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3
replies
1.2k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 19 months ago by ▴ 780 • written 19 months ago by • 0
0
votes
14
replies
4.0k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 15 months ago by • 0 • written 20 months ago by • 0
1
vote
1
reply
826
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 20 months ago by 68k • written 20 months ago by ▴ 10
0
votes
3
replies
1.6k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 23 months ago by ▴ 780 • written 23 months ago by ▴ 10
0
votes
2
replies
914
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 13 months ago by • 0 • written 23 months ago by • 0
0
votes
1
reply
905
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
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0
replies
661
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.1 years ago edward.esiribloom • 0
6
votes
6
replies
9.7k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 50
0
votes
1
reply
958
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
4
replies
1.7k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
3
replies
1.5k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
5
replies
2.0k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.2 years ago by • 0
0
votes
1
reply
1.3k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
votes
3
replies
1.8k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.3 years ago by ▴ 40 • written 2.3 years ago by • 0
0
votes
1
reply
1.5k
views
minfi read.metharray.sheet error
minfi
updated 2.4 years ago by 68k • written 2.4 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 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
0
replies
853
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.7 years ago calen.p.ryan • 0
0
votes
0
replies
981
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.9 years ago runye • 0
0
votes
1
reply
1.4k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
votes
3
replies
1.6k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.1 years ago • updated 3.0 years ago ramonfallon ▴ 20
0
votes
2
replies
3.4k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.0 years ago by • 0 • written 9.6 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.0 years ago octaviompa • 0
0
votes
0
replies
855
views
Minfi package: controlStripPlot colors
minfi
3.2 years ago Rebecca • 0
0
votes
1
reply
1.3k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
9
replies
4.0k
views
clarification about bumphunter value output
minfi bumphunter
updated 23 months ago by • 0 • written 7.2 years ago by • 0
0
votes
1
reply
1.3k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
0
votes
0
replies
1.1k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.7 years ago ponche_de_kiwi • 0
50 results • Page 1 of 1
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Comment: DESeq2 with proteomics data by wook2014 • 0
You may need to do NA imputation before give the data to DEseq2 and there are study on DEseq2 performance on proteomics data, like :https:/…
Answer: Unable to install a forged BSgenome package by James W. MacDonald 68k
Add a repos = NULL to `install.packages`. You may also need to either move the file to a dir that doesn't have a space in the name or you […
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
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Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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