Showing : minfi • reset
0
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62
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Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
8 weeks ago kyleyxw • 0
2
votes
2
replies
134
views
How to overcome issue linked to loading big R object
minfi R methylation
12 weeks ago Federica ▴ 10
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votes
0
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127
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shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
3 months ago Jeff ▴ 20
0
votes
1
reply
168
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest minfi conumee
updated 12 weeks ago by ▴ 40 • written 3 months ago by • 0
1
vote
8
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271
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3 months ago chay • 0
0
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1
reply
259
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 5 months ago by • 0 • written 5 months ago by • 0
1
vote
4
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256
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Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
5 months ago shweta • 0
0
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2
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1.3k
views
minfi - error when reading idat files
minfi methylation
updated 5 months ago by • 0 • written 4.1 years ago by ▴ 10
0
votes
9
replies
328
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 6 months ago by ★ 5.0k • written 6 months ago by ▴ 160
0
votes
2
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239
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Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC arrays limma minfi Epigenetics
updated 8 months ago by 43k • written 8 months ago by ▴ 20
0
votes
6
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261
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NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 8 months ago by 6.5k • written 8 months ago by • 0
0
votes
2
replies
177
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Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
15 months ago • updated 9 months ago Nala • 0
0
votes
9
replies
1.1k
views
clarification about bumphunter value output
minfi bumphunter
written 3.4 years ago by • 0
1
vote
3
replies
459
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 10 months ago by 57k • written 10 months ago by ▴ 50
0
votes
0
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86
views
Inter-chip methylation normalization
minfi
16 months ago blawney • 0
0
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1
reply
152
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi cell proportion estimateCellCounts DNA Methylation
16 months ago grayapply2009 • 0
0
votes
4
replies
170
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
18 months ago • updated 17 months ago i.s.brorson • 0
3
votes
3
replies
2.8k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 3 months ago by • 0 • written 2.0 years ago by ▴ 10
0
votes
1
reply
349
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 23 months ago by 57k • written 23 months ago by • 0
1
vote
3
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300
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
0
votes
3
replies
279
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 2.0 years ago by ★ 27k • written 2.0 years ago by • 0
0
votes
1
reply
272
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
2.1 years ago Boran Gao • 0
0
votes
2
replies
334
views
[read.metharray] Trying to parse different IDAT files, of different size and type.
limma minfi
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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2
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936
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3 months ago by • 0 • written 2.2 years ago by • 0
0
votes
1
reply
320
views
Unable to run dmp <- dmpFinder() function with R 3.6
normalization News minfi
updated 2.2 years ago by 2.8k • written 2.2 years ago by • 0
0
votes
0
replies
280
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
2.4 years ago rmf ▴ 20
0
votes
0
replies
277
views
Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
2.4 years ago rmf ▴ 20
1
vote
1
reply
249
views
Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 2.4 years ago by 57k • written 2.4 years ago by • 0
4
votes
4
replies
405
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.4 years ago by 6.5k • written 2.4 years ago by • 0
1
vote
6
replies
602
views
Reading 450k data in minfi
450K minfi
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
348
views
Loading packages in R minfi, limma
limma minfi
updated 2.4 years ago by ▴ 240 • written 2.4 years ago by • 0
0
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0
replies
677
views
Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
2.4 years ago lalchungnungabt17 • 0
0
votes
1
reply
315
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
1
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2
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541
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.6 years ago by ★ 1.2k • written 2.6 years ago by • 0
0
votes
1
reply
610
views
Can not install MINFI in WinDow 10 correctly
minfi Error: package ‘bumphunter’ could not be loaded
updated 2.8 years ago by 57k • written 2.8 years ago by • 0
1
vote
2
replies
801
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 2.9 years ago by 57k • written 2.9 years ago by ▴ 20
0
votes
0
replies
450
views
estimateCellCounts issue with EPIC array data in minfi
minfi estimatecellcounts
2.9 years ago a.webster • 0
0
votes
4
replies
516
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 2.9 years ago by 6.5k • written 2.9 years ago by • 0
0
votes
5
replies
776
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 2.9 years ago by ▴ 240 • written 2.9 years ago by ▴ 50
0
votes
3
replies
574
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
3.0 years ago jbar3141 • 0
1
vote
2
replies
481
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi normalization outliers dna methylation densityplot
3.0 years ago peter.fransquet • 0
0
votes
1
reply
355
views
Minci fails to install on Linux CentOS
R minfi package installation
3.0 years ago barbaraheude • 0
0
votes
7
replies
900
views
Minfi read.metharray error in checkslotassignment
minfi read.metharray.exp
updated 3.0 years ago by • 0 • written 3.9 years ago by • 0
0
votes
0
replies
469
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
3.0 years ago sichan • 0
0
votes
1
reply
880
views
getSex error even when sex is provided
minfi estimatecellcounts getSex preprocessQuantile
updated 3.1 years ago by 6.5k • written 3.1 years ago by • 0
0
votes
3
replies
499
views
QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 3.1 years ago by ▴ 240 • written 3.1 years ago by ▴ 180
0
votes
0
replies
468
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
3.2 years ago daniel.green • 0
0
votes
1
reply
605
views
ChAMP functional normalization error "subscript out of bounds"
champ epic microarray normalization minfi
3.2 years ago Laura • 0
0
votes
3
replies
1.2k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation minfi bumphunter
updated 3.2 years ago by ▴ 470 • written 3.2 years ago by • 0
2
votes
6
replies
734
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 3.2 years ago by ▴ 120 • written 3.2 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Selecting pairs of exons from differentially spliced genes by jamie.gearing ▴ 40
That is fair enough. Sensible is always reassuring to hear! Thanks very much for your input Gordon. Best regards, Jamie.
Answer: Selecting pairs of exons from differentially spliced genes by Gordon Smyth 43k
Choosing a representative pair of exons is not part of our method, so we won't make any recommendations. You should choose the exons wit…
Comment: combineTwoExpressionSet from a4Base is not working properly by russ.bainer • 0
I ran across this bug as well- the issue is related to the code failing to reorder the ExpressionSet rows prior to merging. A workaround fo…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
k has to be odd - trying 9, 21 instead
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…
Votes
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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