Showing : Minfi • reset
1
vote
2
replies
490
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
11 days ago user_bioinfo • 0
4
votes
8
replies
1.1k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
3 months ago • updated 13 days ago xiaofeiwang198266 • 0
1
vote
4
replies
538
views
Handling Epic Array Data
minfi
3 months ago Melisa Tecik • 0
2
votes
2
replies
432
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
3 months ago Rakesh • 0
2
votes
5
replies
641
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 4 months ago by 68k • written 4 months ago by • 0
0
votes
2
replies
633
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 6 months ago by • 0 • written 6 months ago by • 0
3
votes
12
replies
4.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 7 months ago by ▴ 230 • written 15 months ago by ▴ 10
0
votes
1
reply
519
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
0
replies
473
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
8 months ago pcibin • 0
0
votes
2
replies
787
views
Epicv2 conversion fail
minfi
8 months ago Alex • 0
2
votes
3
replies
1.6k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 8 weeks ago by • 0 • written 10 months ago by • 0
1
vote
4
replies
607
views
minfi::read.metharray.exp
minfiData minfi
updated 10 months ago by ▴ 780 • written 10 months ago by • 0
0
votes
4
replies
778
views
Minfi - estimatecellscount
min minfi
updated 10 months ago by 68k • written 11 months ago by • 0
0
votes
0
replies
617
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
12 months ago Felix • 0
0
votes
1
reply
470
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
7
replies
1.1k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
2
replies
2.2k
views
EPIC array hg38 annotation?
minfi DMRcate
12 months ago mycetes • 0
0
votes
0
replies
813
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
14 months ago kyj2226 • 0
3
votes
2
replies
1.0k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
14 months ago kyj2226 • 0
0
votes
1
reply
714
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 15 months ago by ▴ 780 • written 15 months ago by • 0
0
votes
5
replies
1.5k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
16 months ago dorota.komar • 0
0
votes
2
replies
1.2k
views
minfi differential methylation analysis errors
minfi
16 months ago matthew.sinton • 0
0
votes
3
replies
1.1k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
votes
14
replies
3.7k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 13 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
745
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
3
replies
1.5k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 21 months ago by ▴ 780 • written 21 months ago by ▴ 10
0
votes
2
replies
872
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 11 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
833
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 23 months ago by 52k • written 23 months ago by • 0
0
votes
0
replies
634
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
23 months ago edward.esiribloom • 0
6
votes
6
replies
9.1k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 4 months ago by • 0 • written 23 months ago by ▴ 50
0
votes
1
reply
916
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 24 months ago by 68k • written 24 months ago by • 0
0
votes
4
replies
1.6k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 24 months ago by 68k • written 24 months ago by • 0
1
vote
3
replies
1.4k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 24 months ago by 68k • written 24 months ago by • 0
0
votes
5
replies
1.9k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 24 months ago by • 0
0
votes
1
reply
1.2k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
2
votes
3
replies
1.6k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.2 years ago by ▴ 40 • written 2.2 years ago by • 0
0
votes
1
reply
1.4k
views
minfi read.metharray.sheet error
minfi
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
1
reply
1.4k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
0
replies
803
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.6 years ago calen.p.ryan • 0
0
votes
0
replies
947
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
2.7 years ago runye • 0
0
votes
1
reply
1.3k
views
what is the format of DMPfinder in minfi package
minfi
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
3
replies
1.5k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.9 years ago • updated 2.8 years ago ramonfallon ▴ 20
0
votes
2
replies
3.3k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.9 years ago by • 0 • written 9.4 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.9 years ago octaviompa • 0
0
votes
0
replies
829
views
Minfi package: controlStripPlot colors
minfi
3.0 years ago Rebecca • 0
0
votes
1
reply
1.2k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
9
replies
3.8k
views
clarification about bumphunter value output
minfi bumphunter
updated 21 months ago by • 0 • written 7.0 years ago by • 0
0
votes
1
reply
1.2k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
0
replies
1.1k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.6 years ago ponche_de_kiwi • 0
3
votes
6
replies
2.2k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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