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EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 3 months ago by ▴ 160 • written 3 months ago by • 0
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130
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
5 months ago ponche_de_kiwi • 0
3
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6
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273
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Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 5 months ago by 58k • written 5 months ago by • 0
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0
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152
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Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
7 months ago kyleyxw • 0
2
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2
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245
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How to overcome issue linked to loading big R object
minfi R methylation
8 months ago Federica ▴ 10
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0
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212
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shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
9 months ago Jeff ▴ 20
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1
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317
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest minfi conumee
updated 8 months ago by ▴ 40 • written 9 months ago by • 0
1
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8
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427
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
9 months ago chay • 0
0
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1
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473
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 10 months ago by • 0 • written 10 months ago by • 0
1
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4
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483
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Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
11 months ago shweta • 0
0
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2
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1.5k
views
minfi - error when reading idat files
minfi methylation
updated 11 months ago by • 0 • written 4.5 years ago by ▴ 10
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9
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563
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Rhdf5lib installation problem
minfi Rhdf5lib
updated 12 months ago by ★ 5.3k • written 12 months ago by ▴ 160
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2
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380
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Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC arrays limma minfi Epigenetics
updated 14 months ago by 44k • written 14 months ago by ▴ 20
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6
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403
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NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 14 months ago by 6.5k • written 14 months ago by • 0
0
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2
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291
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Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
21 months ago • updated 14 months ago Nala • 0
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9
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1.4k
views
clarification about bumphunter value output
minfi bumphunter
written 3.9 years ago by • 0
1
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3
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728
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normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 16 months ago by 58k • written 16 months ago by ▴ 50
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0
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150
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Inter-chip methylation normalization
minfi
21 months ago blawney • 0
0
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1
reply
256
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi cell proportion estimateCellCounts DNA Methylation
22 months ago grayapply2009 • 0
0
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4
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270
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Fix regions for bumphunter
bumphunter DMR methylation minfi
23 months ago i.s.brorson • 0
4
votes
3
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3.9k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 9 months ago by • 0 • written 2.5 years ago by ▴ 10
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1
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523
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 2.4 years ago by 58k • written 2.4 years ago by • 0
1
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3
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444
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by • 0
0
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3
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390
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
0
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1
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386
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
2.5 years ago Boran Gao • 0
0
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2
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460
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[read.metharray] Trying to parse different IDAT files, of different size and type.
limma minfi
updated 2.6 years ago by 44k • written 2.6 years ago by • 0
1
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2
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1.4k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 9 months ago by • 0 • written 2.7 years ago by • 0
0
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1
reply
399
views
Unable to run dmp <- dmpFinder() function with R 3.6
normalization News minfi
updated 2.7 years ago by 2.9k • written 2.7 years ago by • 0
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0
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393
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
2.8 years ago rmf ▴ 20
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0
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365
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Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
2.8 years ago rmf ▴ 20
1
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1
reply
318
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Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 2.9 years ago by 58k • written 2.9 years ago by • 0
4
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4
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514
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.9 years ago by 6.5k • written 2.9 years ago by • 0
1
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6
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760
views
Reading 450k data in minfi
450K minfi
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
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1
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417
views
Loading packages in R minfi, limma
limma minfi
updated 2.9 years ago by ▴ 240 • written 2.9 years ago by • 0
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0
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860
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
2.9 years ago lalchungnungabt17 • 0
0
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1
reply
375
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 3.0 years ago by 58k • written 3.0 years ago by • 0
1
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2
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730
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 3.1 years ago by ★ 1.3k • written 3.1 years ago by • 0
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1
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776
views
Can not install MINFI in WinDow 10 correctly
minfi Error: package ‘bumphunter’ could not be loaded
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
1
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2
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1.0k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 3.3 years ago by 58k • written 3.3 years ago by ▴ 20
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548
views
estimateCellCounts issue with EPIC array data in minfi
minfi estimatecellcounts
3.4 years ago a.webster • 0
0
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4
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653
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 3.4 years ago by 6.5k • written 3.4 years ago by • 0
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5
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940
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 3.4 years ago by ▴ 240 • written 3.4 years ago by ▴ 50
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3
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738
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
3.4 years ago jbar3141 • 0
1
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2
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580
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi normalization outliers dna methylation densityplot
3.5 years ago peter.fransquet • 0
0
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1
reply
419
views
Minci fails to install on Linux CentOS
R minfi package installation
3.5 years ago barbaraheude • 0
0
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7
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985
views
Minfi read.metharray error in checkslotassignment
minfi read.metharray.exp
updated 3.5 years ago by • 0 • written 4.4 years ago by • 0
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0
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558
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
3.5 years ago sichan • 0
0
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1
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998
views
getSex error even when sex is provided
minfi estimatecellcounts getSex preprocessQuantile
updated 3.6 years ago by 6.5k • written 3.6 years ago by • 0
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3
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625
views
QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 3.6 years ago by ▴ 240 • written 3.6 years ago by ▴ 180
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0
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549
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
3.6 years ago daniel.green • 0
50 results • Page 1 of 1
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Comment: Cannot install Phyloseq and dada2 by Guido Hooiveld ★ 3.2k
Did you notice this message:? Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.0.0/libra…
Comment: Use of shrunken LFCs to address questions about the distribution of LFCs between by i.sudbery ▴ 20
Thanks Mike. I might have a play with stratifying by expression level. One reason I wasn't looking at gene set testing is that its the nul…
Answer: submitting a BSgenome package by deisianyufg • 0
From my Github repository. I am sorry, I thought the package was already released and realize now that is still only in my github reposito…
Comment: PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp by swbarnes2 ▴ 970
Is the one plot a mirror image of the other?
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between by Michael Love 35k
hi Ian, Great question, and good to be concerned that the mean expression may be a confounder for either analysis, Why not stratify your…
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Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between
Answer: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
Comment: submitting a BSgenome package
Answer: rlog vs vst for outlier identification
Answer: DESeq2 median of ratios normalization for signature score calculation
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