Showing : minfi • reset
0
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5
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
21 minutes ago e1271094 • 0
1
vote
4
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209
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minfi::read.metharray.exp
minfiData minfi
updated 13 days ago by ▴ 780 • written 14 days ago by • 0
0
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4
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247
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Minfi - estimatecellscount
min minfi
updated 7 days ago by 65k • written 5 weeks ago by • 0
0
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0
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194
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Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
8 weeks ago Felix • 0
0
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1
reply
182
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Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
0
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7
replies
463
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error in reading idat files and creating rgset
minfi MethylationArray
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
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2
replies
538
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EPIC array hg38 annotation?
minfi DMRcate
12 weeks ago mycetes • 0
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0
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260
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
3
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2
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464
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What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
4 months ago kyj2226 • 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
0
votes
1
reply
327
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
0
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2
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664
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minfi differential methylation analysis errors
minfi
6 months ago matthew.sinton • 0
0
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5
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926
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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
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3
replies
567
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
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14
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1.9k
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Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
398
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 8 months ago by 65k • written 8 months ago by • 0
0
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3
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941
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Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 11 months ago by ▴ 780 • written 11 months ago by ▴ 10
0
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2
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572
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 6 weeks ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
544
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 13 months ago by 50k • written 13 months ago by • 0
0
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0
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414
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
13 months ago edward.esiribloom • 0
6
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5
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6.0k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 6 months ago by ▴ 10 • written 13 months ago by ▴ 50
0
votes
1
reply
615
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
4
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1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 14 months ago by 65k • written 14 months ago by • 0
0
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5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 14 months ago by • 0
1
vote
3
replies
836
views
Analysing Genome Studio .txt files with minfi
minfi
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
1
reply
709
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
943
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
0
votes
1
reply
998
views
minfi read.metharray.sheet error
minfi
updated 17 months ago by 65k • written 17 months ago by • 0
0
votes
1
reply
940
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
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0
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542
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
21 months ago calen.p.ryan • 0
0
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0
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712
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
23 months ago runye • 0
0
votes
1
reply
904
views
what is the format of DMPfinder in minfi package
minfi
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
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0
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924
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Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.0 years ago octaviompa • 0
0
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3
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1.2k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.1 years ago • updated 23 months ago ramonfallon ▴ 20
0
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0
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645
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago Rebecca • 0
0
votes
1
reply
836
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
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1
reply
884
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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0
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741
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
2.7 years ago ponche_de_kiwi • 0
3
votes
6
replies
1.7k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
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0
replies
767
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
872
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
0
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0
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796
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
3.1 years ago Jeff ▴ 20
0
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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 3.1 years ago by • 0
1
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8
replies
1.4k
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.1 years ago chay • 0
0
votes
1
reply
2.0k
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 3.2 years ago by • 0 • written 3.2 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
0
votes
9
replies
2.8k
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 3.5 years ago by 50k • written 3.5 years ago by ▴ 20
0
votes
6
replies
1.5k
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 3.5 years ago by ★ 6.5k • written 3.5 years ago by • 0
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
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