Showing : minfi • reset
1
vote
4
replies
140
views
minfi::read.metharray.exp
minfiData minfi
updated 2 days ago by ▴ 780 • written 4 days ago by • 0
0
votes
2
replies
165
views
Minfi - estimatecellscount
min minfi
28 days ago clacarion • 0
0
votes
0
replies
177
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
7 weeks ago Felix • 0
0
votes
1
reply
171
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
votes
7
replies
430
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
2
replies
473
views
EPIC array hg38 annotation?
minfi DMRcate
11 weeks ago • updated 10 weeks ago mycetes • 0
0
votes
0
replies
244
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
3
votes
2
replies
453
views
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
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 23 days ago by ▴ 170 • written 5 months ago by ▴ 10
0
votes
1
reply
299
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
0
votes
2
replies
639
views
minfi differential methylation analysis errors
minfi
6 months ago matthew.sinton • 0
0
votes
5
replies
893
views
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
votes
3
replies
537
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 6 months ago by ▴ 780 • written 6 months ago by • 0
0
votes
14
replies
1.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 12 weeks ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
386
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
3
replies
917
views
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
votes
2
replies
561
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 4 weeks ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
536
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 12 months ago by 50k • written 13 months ago by • 0
0
votes
0
replies
405
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
13 months ago edward.esiribloom • 0
4
votes
5
replies
5.8k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 5 months ago by • 0 • written 13 months ago by ▴ 50
0
votes
1
reply
598
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
4
replies
1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 13 months ago by • 0
1
vote
3
replies
807
views
Analysing Genome Studio .txt files with minfi
minfi
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
1
reply
687
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
916
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
0
votes
1
reply
980
views
minfi read.metharray.sheet error
minfi
updated 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
920
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
votes
0
replies
535
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
20 months ago calen.p.ryan • 0
0
votes
0
replies
702
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
22 months ago runye • 0
0
votes
1
reply
884
views
what is the format of DMPfinder in minfi package
minfi
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
votes
0
replies
902
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.0 years ago octaviompa • 0
0
votes
3
replies
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
votes
0
replies
636
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago Rebecca • 0
0
votes
1
reply
825
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
votes
1
reply
875
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
votes
0
replies
729
views
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
votes
0
replies
757
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
859
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
0
votes
0
replies
784
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
3.0 years ago Jeff ▴ 20
0
votes
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
vote
8
replies
1.4k
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.1 years ago • updated 3.0 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
2.7k
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 3.4 years ago by 50k • written 3.4 years ago by ▴ 20
0
votes
6
replies
1.4k
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
0
votes
2
replies
1.0k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
4.0 years ago • updated 3.5 years ago Nala • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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