Showing : Minfi • reset
3
votes
6
replies
2.5k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
votes
0
replies
1.1k
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
4.3 years ago kyleyxw • 0
2
votes
2
replies
1.3k
views
How to overcome issue linked to loading big R object
minfi R methylation
4.4 years ago Federica ▴ 10
0
votes
0
replies
1.1k
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
4.4 years ago Jeff ▴ 20
0
votes
1
reply
2.1k
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest minfi conumee
updated 4.4 years ago by ▴ 40 • written 4.5 years ago by • 0
1
vote
8
replies
2.1k
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
4.5 years ago • updated 4.4 years ago chay • 0
1
vote
1
reply
2.8k
views
plotSex error message
minfiData plotsex minfi minfiDataEPIC r
updated 4.6 years ago by • 0 • written 4.6 years ago by • 0
1
vote
4
replies
3.7k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
4.6 years ago shweta • 0
1
vote
5
replies
5.4k
views
minfi - error when reading idat files
minfi methylation
updated 3.0 years ago by • 0 • written 8.2 years ago by ▴ 10
0
votes
9
replies
4.4k
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 4.7 years ago by ★ 6.6k • written 4.7 years ago by ▴ 160
0
votes
2
replies
2.7k
views
Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC arrays limma minfi Epigenetics
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 20
0
votes
6
replies
2.2k
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 4.8 years ago by ★ 6.5k • written 4.9 years ago by • 0
0
votes
2
replies
1.4k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
5.4 years ago • updated 4.9 years ago Nala • 0
1
vote
3
replies
4.0k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 50
0
votes
0
replies
773
views
Inter-chip methylation normalization
minfi
5.5 years ago blawney • 0
0
votes
1
reply
1.3k
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi cell proportion estimateCellCounts DNA Methylation
5.5 years ago grayapply2009 • 0
0
votes
4
replies
1.4k
views
Fix regions for bumphunter
bumphunter DMR methylation minfi
5.6 years ago i.s.brorson • 0
7
votes
3
replies
13k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 2.5 years ago by • 0 • written 6.2 years ago by ▴ 10
0
votes
1
reply
2.7k
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
1
vote
3
replies
2.1k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
0
votes
3
replies
1.7k
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 6.2 years ago by ★ 29k • written 6.2 years ago by • 0
0
votes
1
reply
1.3k
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
6.2 years ago Boran Gao • 0
0
votes
2
replies
2.0k
views
[read.metharray] Trying to parse different IDAT files, of different size and type.
limma minfi
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
1
vote
2
replies
4.8k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 4.4 years ago by • 0 • written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
Unable to run dmp <- dmpFinder() function with R 3.6
normalization News minfi
updated 6.3 years ago by 4.2k • written 6.3 years ago by • 0
0
votes
0
replies
1.5k
views
Beta values and M values cluster differently
methylationEPIC minfi microarray epigenetics EPIC
6.5 years ago firestar ▴ 20
0
votes
0
replies
1.1k
views
Best normalisation method
microarray methylationEPIC epigenetics minfi EPIC
6.5 years ago firestar ▴ 20
1
vote
1
reply
1.0k
views
Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
4
votes
4
replies
1.8k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 6.5 years ago by ★ 6.5k • written 6.5 years ago by • 0
1
vote
6
replies
2.8k
views
Reading 450k data in minfi
450K minfi
updated 6.5 years ago by • 0 • written 6.6 years ago by • 0
0
votes
1
reply
1.1k
views
Loading packages in R minfi, limma
limma minfi
updated 6.5 years ago by ▴ 290 • written 6.5 years ago by • 0
0
votes
0
replies
2.5k
views
Reading csv file in minfi
minfi Tutorial infinium450K
updated 8 days ago by 43k • written 6.6 years ago by • 0
0
votes
1
reply
1.3k
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
1
vote
2
replies
1.8k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 6.8 years ago by ★ 1.3k • written 6.8 years ago by • 0
0
votes
1
reply
1.8k
views
Can not install MINFI in WinDow 10 correctly
minfi Error: package ‘bumphunter’ could not be loaded
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
1
vote
2
replies
2.4k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 20
0
votes
0
replies
1.3k
views
estimateCellCounts issue with EPIC array data in minfi
minfi estimatecellcounts
7.1 years ago a.webster • 0
0
votes
4
replies
1.6k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 7.1 years ago by ★ 6.5k • written 7.1 years ago by • 0
0
votes
5
replies
2.9k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 7.1 years ago by ▴ 290 • written 7.1 years ago by ▴ 60
0
votes
3
replies
2.0k
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
7.1 years ago jbar3141 • 0
1
vote
2
replies
1.9k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi normalization outliers dna methylation densityplot
7.2 years ago peter.fransquet • 0
0
votes
1
reply
1.1k
views
Minci fails to install on Linux CentOS
R minfi package installation
7.2 years ago barbaraheude • 0
0
votes
7
replies
1.7k
views
Minfi read.metharray error in checkslotassignment
minfi read.metharray.exp
updated 7.2 years ago by • 0 • written 8.1 years ago by • 0
0
votes
0
replies
1.5k
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
7.2 years ago sichan • 0
0
votes
1
reply
2.4k
views
getSex error even when sex is provided
minfi estimatecellcounts getSex preprocessQuantile
updated 7.3 years ago by ★ 6.5k • written 7.3 years ago by • 0
0
votes
3
replies
1.9k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 7.3 years ago by ▴ 290 • written 7.3 years ago by ▴ 190
0
votes
0
replies
1.4k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
7.3 years ago daniel.green • 0
0
votes
1
reply
1.7k
views
ChAMP functional normalization error "subscript out of bounds"
champ epic microarray normalization minfi
7.3 years ago Laura • 0
0
votes
3
replies
2.6k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation minfi bumphunter
updated 7.4 years ago by ▴ 760 • written 7.4 years ago by • 0
2
votes
6
replies
2.6k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 7.4 years ago by ▴ 230 • written 7.4 years ago by • 0
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Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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