Showing : Minfi • reset
1
vote
4
replies
343
views
Handling Epic Array Data
minfi
5 days ago • updated 4 days ago Melisa Tecik • 0
2
votes
2
replies
244
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
6 days ago • updated 5 days ago Rakesh • 0
2
votes
5
replies
449
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
0
votes
2
replies
457
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 3 months ago by • 0 • written 3 months ago by • 0
3
votes
12
replies
3.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 months ago by ▴ 200 • written 12 months ago by ▴ 10
0
votes
1
reply
399
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 4 months ago by 67k • written 4 months ago by • 0
0
votes
0
replies
349
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
4 months ago pcibin • 0
0
votes
2
replies
576
views
Epicv2 conversion fail
minfi
5 months ago • updated 4 months ago Alex • 0
2
votes
2
replies
1.1k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 6 weeks ago by • 0 • written 6 months ago by • 0
1
vote
4
replies
497
views
minfi::read.metharray.exp
minfiData minfi
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
4
replies
589
views
Minfi - estimatecellscount
min minfi
updated 6 months ago by 67k • written 8 months ago by • 0
0
votes
0
replies
511
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
8 months ago Felix • 0
0
votes
1
reply
386
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
880
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 9 months ago by 67k • written 9 months ago by • 0
1
vote
2
replies
1.7k
views
EPIC array hg38 annotation?
minfi DMRcate
9 months ago mycetes • 0
0
votes
0
replies
580
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
11 months ago kyj2226 • 0
3
votes
2
replies
873
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
11 months ago kyj2226 • 0
0
votes
1
reply
628
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 12 months ago by ▴ 780 • written 12 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
13 months ago dorota.komar • 0
0
votes
2
replies
1.1k
views
minfi differential methylation analysis errors
minfi
13 months ago matthew.sinton • 0
0
votes
3
replies
976
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 13 months ago by ▴ 780 • written 13 months ago by • 0
0
votes
14
replies
3.3k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 10 months ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
625
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 15 months ago by 67k • written 15 months ago by • 0
0
votes
3
replies
1.3k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 18 months ago by ▴ 780 • written 18 months ago by ▴ 10
0
votes
2
replies
790
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 8 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
724
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 20 months ago by 51k • written 20 months ago by • 0
0
votes
0
replies
570
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
20 months ago edward.esiribloom • 0
6
votes
6
replies
8.2k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 6 weeks ago by • 0 • written 20 months ago by ▴ 50
0
votes
1
reply
851
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
4
replies
1.4k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 20 months ago by 67k • written 20 months ago by • 0
1
vote
3
replies
1.2k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
5
replies
1.7k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 20 months ago by • 0
0
votes
1
reply
1.0k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 21 months ago by 67k • written 21 months ago by • 0
2
votes
3
replies
1.4k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 22 months ago by ▴ 40 • written 23 months ago by • 0
0
votes
1
reply
1.3k
views
minfi read.metharray.sheet error
minfi
updated 23 months ago by 67k • written 23 months 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
710
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.3 years ago calen.p.ryan • 0
0
votes
0
replies
895
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 2.5 years ago by ▴ 780 • written 2.5 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 2.5 years ago ramonfallon ▴ 20
0
votes
2
replies
3.1k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.6 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
2.6 years ago octaviompa • 0
0
votes
0
replies
779
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 2.8 years ago by 67k • written 2.8 years ago by • 0
0
votes
9
replies
3.6k
views
clarification about bumphunter value output
minfi bumphunter
updated 18 months ago by • 0 • written 6.7 years ago by • 0
0
votes
1
reply
1.1k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
votes
0
replies
977
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
3.3 years ago ponche_de_kiwi • 0
3
votes
6
replies
2.1k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
0
votes
0
replies
922
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3.5 years ago kyleyxw • 0
2
votes
2
replies
1.1k
views
How to overcome issue linked to loading big R object
minfi R methylation
3.6 years ago Federica ▴ 10
50 results • Page 1 of 1
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Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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