Showing : minfi • reset
0
votes
5
replies
365
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
20 days ago • updated 2 days ago xiaofeiwang198266 • 0
1
vote
4
replies
424
views
Handling Epic Array Data
minfi
4 weeks ago Melisa Tecik • 0
2
votes
2
replies
318
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
4 weeks ago Rakesh • 0
2
votes
5
replies
500
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
0
votes
2
replies
497
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 4 months ago by • 0 • written 4 months ago by • 0
3
votes
12
replies
3.8k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 5 months ago by ▴ 200 • written 13 months ago by ▴ 10
0
votes
1
reply
426
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
0
replies
376
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
5 months ago pcibin • 0
0
votes
2
replies
633
views
Epicv2 conversion fail
minfi
6 months ago • updated 5 months ago Alex • 0
2
votes
2
replies
1.3k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 10 weeks ago by • 0 • written 7 months ago by • 0
1
vote
4
replies
529
views
minfi::read.metharray.exp
minfiData minfi
updated 8 months ago by ▴ 780 • written 8 months ago by • 0
0
votes
4
replies
645
views
Minfi - estimatecellscount
min minfi
updated 7 months ago by 67k • written 8 months ago by • 0
0
votes
0
replies
538
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
9 months ago Felix • 0
0
votes
1
reply
411
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 9 months ago by 67k • written 9 months ago by • 0
0
votes
7
replies
944
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 10 months ago by 67k • written 10 months ago by • 0
1
vote
2
replies
1.8k
views
EPIC array hg38 annotation?
minfi DMRcate
10 months ago mycetes • 0
0
votes
0
replies
643
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
12 months ago kyj2226 • 0
3
votes
2
replies
918
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
12 months ago kyj2226 • 0
0
votes
1
reply
654
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 13 months ago by ▴ 780 • written 13 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
14 months ago dorota.komar • 0
0
votes
2
replies
1.1k
views
minfi differential methylation analysis errors
minfi
14 months ago matthew.sinton • 0
0
votes
3
replies
1.0k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
14
replies
3.4k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 10 months ago by • 0 • written 16 months ago by • 0
0
votes
1
reply
648
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 16 months ago by 67k • written 16 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 19 months ago by ▴ 780 • written 19 months ago by ▴ 10
0
votes
2
replies
812
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 9 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
748
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 20 months ago by 52k • written 21 months ago by • 0
0
votes
0
replies
590
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
21 months ago edward.esiribloom • 0
6
votes
6
replies
8.5k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 10 weeks ago by • 0 • written 21 months ago by ▴ 50
0
votes
1
reply
868
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 21 months ago by 67k • written 21 months ago by • 0
0
votes
4
replies
1.5k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 21 months ago by 67k • written 21 months ago by • 0
1
vote
3
replies
1.3k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 21 months ago by 67k • written 21 months ago by • 0
0
votes
5
replies
1.7k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 21 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 22 months ago by 67k • written 22 months ago by • 0
2
votes
3
replies
1.4k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 23 months ago by ▴ 40 • written 23 months ago by • 0
0
votes
1
reply
1.3k
views
minfi read.metharray.sheet error
minfi
updated 2.0 years ago by 67k • written 2.0 years ago by • 0
0
votes
1
reply
1.3k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
0
votes
0
replies
732
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.4 years ago calen.p.ryan • 0
0
votes
0
replies
912
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.5 years ago runye • 0
0
votes
1
reply
1.2k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
votes
3
replies
1.4k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.7 years ago • updated 2.6 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 2.7 years ago by • 0 • written 9.2 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.7 years ago octaviompa • 0
0
votes
0
replies
793
views
Minfi package: controlStripPlot colors
minfi
2.8 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 2.9 years ago by 67k • written 2.9 years ago by • 0
0
votes
9
replies
3.7k
views
clarification about bumphunter value output
minfi bumphunter
updated 19 months ago by • 0 • written 6.8 years ago by • 0
0
votes
1
reply
1.1k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
0
votes
0
replies
997
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.4 years ago ponche_de_kiwi • 0
3
votes
6
replies
2.1k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 3.4 years ago by 67k • written 3.4 years ago by • 0
0
votes
0
replies
946
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3.6 years ago kyleyxw • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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