Showing : minfi • reset
2
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3
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131
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GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 21 days ago by ▴ 30 • written 22 days ago by • 0
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1
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96
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minfi read.metharray.sheet error
minfi
updated 6 weeks ago by 62k • written 6 weeks ago by • 0
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1
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226
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Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 5 months ago by 62k • written 5 months ago by • 0
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0
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133
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
5 months ago calen.p.ryan • 0
0
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0
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195
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Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
7 months ago runye • 0
0
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1
reply
266
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what is the format of DMPfinder in minfi package
minfi
updated 8 months ago by ▴ 530 • written 8 months ago by • 0
0
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3
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523
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methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
10 months ago • updated 8 months ago ramonfallon • 0
0
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2
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1.9k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 9 months ago by • 0 • written 7.3 years ago by ▴ 10
0
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0
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318
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Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
9 months ago octaviompa • 0
0
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0
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325
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Minfi package: controlStripPlot colors
minfi
11 months ago Rebecca • 0
0
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1
reply
391
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Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 11 months ago by 62k • written 11 months ago by • 0
0
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9
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2.1k
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clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 4.9 years ago by • 0
0
votes
1
reply
367
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 15 months ago by ▴ 530 • written 15 months ago by • 0
0
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0
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363
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
17 months ago ponche_de_kiwi • 0
3
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6
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733
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 17 months ago by 62k • written 17 months ago by • 0
0
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0
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399
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Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
20 months ago kyleyxw • 0
2
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2
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455
views
How to overcome issue linked to loading big R object
minfi R methylation
21 months ago Federica ▴ 10
0
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0
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411
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shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
21 months ago Jeff ▴ 20
0
votes
1
reply
632
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest minfi conumee
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
1
vote
8
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708
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
22 months ago • updated 21 months ago chay • 0
0
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1
reply
972
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 23 months ago by • 0 • written 23 months ago by • 0
1
vote
4
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1.2k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
23 months ago shweta • 0
1
vote
5
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2.5k
views
minfi - error when reading idat files
minfi methylation
updated 4 months ago by • 0 • written 5.6 years ago by ▴ 10
0
votes
9
replies
1.2k
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 2.0 years ago by ★ 5.8k • written 2.0 years ago by ▴ 160
0
votes
2
replies
875
views
Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC arrays limma minfi Epigenetics
updated 2.2 years ago by 47k • written 2.2 years ago by ▴ 20
0
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6
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686
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 2.2 years ago by 6.5k • written 2.2 years ago by • 0
0
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2
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523
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
2.8 years ago • updated 2.2 years ago Nala • 0
1
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3
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1.4k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 50
0
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0
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266
views
Inter-chip methylation normalization
minfi
2.8 years ago blawney • 0
0
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1
reply
484
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi cell proportion estimateCellCounts DNA Methylation
2.8 years ago grayapply2009 • 0
0
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4
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447
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
3.0 years ago i.s.brorson • 0
5
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3
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6.5k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 22 months ago by ▴ 10 • written 3.5 years ago by ▴ 10
0
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1
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925
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 3.4 years ago by 62k • written 3.4 years ago by • 0
1
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3
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859
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 3.4 years ago by ▴ 10 • written 3.4 years ago by • 0
0
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3
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667
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
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1
reply
613
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
3.6 years ago Boran Gao • 0
0
votes
2
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780
views
[read.metharray] Trying to parse different IDAT files, of different size and type.
limma minfi
updated 3.6 years ago by 47k • written 3.6 years ago by • 0
1
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2
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2.2k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 21 months ago by • 0 • written 3.7 years ago by • 0
0
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1
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565
views
Unable to run dmp <- dmpFinder() function with R 3.6
normalization News minfi
updated 3.7 years ago by 3.4k • written 3.7 years ago by • 0
0
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0
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587
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
3.9 years ago rmf ▴ 20
0
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0
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516
views
Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
3.9 years ago rmf ▴ 20
1
vote
1
reply
449
views
Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 3.9 years ago by 62k • written 3.9 years ago by • 0
4
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4
replies
727
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 3.9 years ago by 6.5k • written 3.9 years ago by • 0
1
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6
replies
1.1k
views
Reading 450k data in minfi
450K minfi
updated 3.9 years ago by • 0 • written 3.9 years ago by • 0
0
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1
reply
570
views
Loading packages in R minfi, limma
limma minfi
updated 3.9 years ago by ▴ 250 • written 3.9 years ago by • 0
0
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0
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1.2k
views
Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
3.9 years ago lalchungnungabt17 • 0
0
votes
1
reply
544
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 4.0 years ago by 62k • written 4.0 years ago by • 0
1
vote
2
replies
937
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 4.1 years ago by ★ 1.3k • written 4.1 years ago by • 0
0
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1
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1.0k
views
Can not install MINFI in WinDow 10 correctly
minfi Error: package ‘bumphunter’ could not be loaded
updated 4.3 years ago by 62k • written 4.3 years ago by • 0
1
vote
2
replies
1.4k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 4.4 years ago by 62k • written 4.4 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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