Showing : minfi • reset
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 17 days ago by ▴ 170 • written 4 months ago by ▴ 10
0
votes
2
replies
156
views
Minfi - estimatecellscount
min minfi
21 days ago clacarion • 0
0
votes
0
replies
162
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
6 weeks ago Felix • 0
0
votes
1
reply
161
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
0
votes
7
replies
410
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
0
votes
2
replies
429
views
EPIC array hg38 annotation?
minfi DMRcate
10 weeks ago • updated 9 weeks ago mycetes • 0
0
votes
0
replies
233
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
3
votes
2
replies
439
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
4 months ago kyj2226 • 0
0
votes
1
reply
286
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 4 months ago by ▴ 770 • written 4 months ago by • 0
0
votes
5
replies
874
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
6 months ago dorota.komar • 0
0
votes
2
replies
628
views
minfi differential methylation analysis errors
minfi
6 months ago matthew.sinton • 0
0
votes
3
replies
520
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 6 months ago by ▴ 770 • written 6 months ago by • 0
0
votes
14
replies
1.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 11 weeks ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
371
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
3
replies
902
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 11 months ago by ▴ 770 • written 11 months ago by ▴ 10
0
votes
2
replies
552
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 25 days ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
528
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
0
replies
397
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
13 months ago edward.esiribloom • 0
4
votes
5
replies
5.7k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 5 months ago by • 0 • written 13 months ago by ▴ 50
0
votes
1
reply
587
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
4
replies
989
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 13 months ago by 65k • written 13 months ago by • 0
1
vote
3
replies
788
views
Analysing Genome Studio .txt files with minfi
minfi
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 13 months ago by • 0
0
votes
1
reply
666
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 14 months ago by 65k • written 14 months ago by • 0
2
votes
3
replies
901
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
0
votes
1
reply
959
views
minfi read.metharray.sheet error
minfi
updated 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
906
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 20 months ago by 65k • written 20 months ago by • 0
0
votes
0
replies
523
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
20 months ago calen.p.ryan • 0
0
votes
0
replies
693
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
22 months ago runye • 0
0
votes
1
reply
874
views
what is the format of DMPfinder in minfi package
minfi
updated 23 months ago by ▴ 770 • written 23 months ago by • 0
0
votes
3
replies
1.1k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.1 years ago • updated 23 months ago ramonfallon ▴ 20
0
votes
2
replies
2.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 24 months ago by • 0 • written 8.6 years ago by ▴ 10
0
votes
0
replies
888
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.0 years ago octaviompa • 0
0
votes
0
replies
630
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago Rebecca • 0
0
votes
1
reply
812
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 10 months ago by • 0 • written 6.1 years ago by • 0
0
votes
1
reply
866
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 2.5 years ago by ▴ 770 • written 2.5 years ago by • 0
0
votes
0
replies
718
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
2.7 years ago ponche_de_kiwi • 0
3
votes
6
replies
1.6k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
votes
0
replies
747
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
2.9 years ago kyleyxw • 0
2
votes
2
replies
851
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
0
votes
0
replies
773
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
3.0 years ago Jeff ▴ 20
0
votes
1
reply
1.4k
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest minfi conumee
updated 3.0 years ago by ▴ 40 • written 3.0 years ago by • 0
1
vote
8
replies
1.4k
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.0 years ago chay • 0
0
votes
1
reply
2.0k
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
1
vote
4
replies
2.7k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
3.2 years ago shweta • 0
1
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
0
votes
9
replies
2.7k
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 3.3 years ago by ★ 6.5k • written 3.3 years ago by ▴ 160
0
votes
2
replies
1.7k
views
Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC arrays limma minfi Epigenetics
updated 3.4 years ago by 50k • written 3.4 years ago by ▴ 20
0
votes
6
replies
1.4k
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 3.4 years ago by ★ 6.5k • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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