Showing : Minfi • reset
0
votes
5
replies
400
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
4 weeks ago • updated 14 days ago xiaofeiwang198266 • 0
1
vote
4
replies
441
views
Handling Epic Array Data
minfi
6 weeks ago Melisa Tecik • 0
2
votes
2
replies
331
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
6 weeks ago Rakesh • 0
2
votes
5
replies
515
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 12 weeks ago by 67k • written 12 weeks ago by • 0
0
votes
2
replies
519
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
432
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
390
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
6 months ago pcibin • 0
0
votes
2
replies
658
views
Epicv2 conversion fail
minfi
6 months ago Alex • 0
2
votes
3
replies
1.4k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 2 days ago by • 0 • written 8 months ago by • 0
1
vote
4
replies
540
views
minfi::read.metharray.exp
minfiData minfi
updated 8 months ago by ▴ 780 • written 8 months ago by • 0
0
votes
4
replies
671
views
Minfi - estimatecellscount
min minfi
updated 8 months ago by 67k • written 9 months ago by • 0
0
votes
0
replies
548
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
10 months ago Felix • 0
0
votes
1
reply
419
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 10 months ago by 67k • written 10 months ago by • 0
0
votes
7
replies
965
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
658
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
12 months ago kyj2226 • 0
3
votes
2
replies
932
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
659
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 15 months ago by ▴ 780 • written 15 months ago by • 0
0
votes
14
replies
3.4k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 11 months ago by • 0 • written 16 months ago by • 0
0
votes
1
reply
661
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
824
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 9 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
757
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 21 months ago by 52k • written 21 months ago by • 0
0
votes
0
replies
596
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
21 months ago edward.esiribloom • 0
6
votes
6
replies
8.6k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 12 weeks ago by • 0 • written 21 months ago by ▴ 50
0
votes
1
reply
878
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 22 months ago by 67k • written 22 months ago by • 0
0
votes
4
replies
1.5k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 22 months ago by 67k • written 22 months ago by • 0
1
vote
3
replies
1.3k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 22 months ago by 67k • written 22 months ago by • 0
0
votes
5
replies
1.7k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 22 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
1.5k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 24 months ago by ▴ 40 • written 24 months ago by • 0
0
votes
1
reply
1.3k
views
minfi read.metharray.sheet error
minfi
updated 2.1 years ago by 67k • written 2.1 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 2.4 years ago by 67k • written 2.4 years ago by • 0
0
votes
0
replies
737
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
918
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.6 years ago runye • 0
0
votes
1
reply
1.3k
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
2.8 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 9.3 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
800
views
Minfi package: controlStripPlot colors
minfi
2.9 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
1.2k
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
1.0k
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
950
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: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Votes
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
Answer: Understanding tximport working with salmon outputs
Answer: enrichGOgradient color change
Awards • All
Popular Question to gingergeiger22 • 0
Popular Question to Gordon Smyth 52k
Popular Question to James W. MacDonald 67k
Popular Question to Chris ▴ 20
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
Seattle, WA, United States, 1 minute ago
The city by the bay, 2 minutes ago
Hong Kong, 27 minutes ago
Switzerland, 33 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 667 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6