Showing : Minfi • reset
0
votes
3
replies
911
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 3 months ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
742
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
6 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
9 months ago • updated 7 months ago xiaofeiwang198266 • 0
1
vote
4
replies
877
views
Handling Epic Array Data
minfi
10 months ago Melisa Tecik • 0
2
votes
2
replies
723
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
10 months ago Rakesh • 0
2
votes
5
replies
944
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
2
replies
950
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 13 months ago by • 0 • written 13 months ago by • 0
4
votes
12
replies
5.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 13 months ago by ▴ 230 • written 22 months ago by ▴ 20
0
votes
1
reply
702
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
0
replies
645
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
14 months ago pcibin • 0
0
votes
2
replies
1.1k
views
Epicv2 conversion fail
minfi
15 months ago • updated 14 months ago Alex • 0
2
votes
4
replies
3.1k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 10 weeks ago by • 0 • written 16 months ago by • 0
1
vote
4
replies
811
views
minfi::read.metharray.exp
minfiData minfi
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
votes
4
replies
967
views
Minfi - estimatecellscount
min minfi
updated 16 months ago by 68k • written 17 months ago by • 0
0
votes
0
replies
748
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
18 months ago Felix • 0
0
votes
1
reply
617
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
7
replies
1.3k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
2
replies
2.9k
views
EPIC array hg38 annotation?
minfi DMRcate
19 months ago mycetes • 0
0
votes
0
replies
1.1k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
21 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
21 months ago kyj2226 • 0
0
votes
1
reply
850
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 22 months ago by ▴ 780 • written 22 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
23 months ago dorota.komar • 0
0
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2
replies
1.5k
views
minfi differential methylation analysis errors
minfi
23 months ago matthew.sinton • 0
0
votes
3
replies
1.3k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
votes
14
replies
4.3k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 19 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 12 weeks 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 2.3 years ago by ▴ 780 • written 2.3 years ago by ▴ 10
0
votes
2
replies
1.0k
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 18 months ago by • 0 • written 2.3 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
739
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.5 years ago edward.esiribloom • 0
6
votes
6
replies
10k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 11 months ago by • 0 • written 2.5 years ago by ▴ 50
0
votes
1
reply
1.0k
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
4
replies
1.9k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
3
replies
1.6k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
5
replies
2.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.5 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
1.9k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.7 years ago by ▴ 40 • written 2.7 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
931
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
3.1 years ago calen.p.ryan • 0
0
votes
0
replies
1.0k
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
3.3 years ago runye • 0
0
votes
1
reply
1.4k
views
what is the format of DMPfinder in minfi package
minfi
updated 3.3 years ago by ▴ 780 • written 3.3 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 3.3 years ago ramonfallon ▴ 20
0
votes
2
replies
3.5k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.4 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
3.4 years ago octaviompa • 0
0
votes
0
replies
912
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 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
9
replies
4.2k
views
clarification about bumphunter value output
minfi bumphunter
updated 2.3 years ago by • 0 • written 7.5 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
4.1 years ago ponche_de_kiwi • 0
281 results • Page 1 of 6
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure by James W. MacDonald 68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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