Showing : minfi • reset
1
vote
1
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100
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 3 days ago by 65k • written 3 days ago by • 0
1
vote
4
replies
213
views
minfi::read.metharray.exp
minfiData minfi
updated 16 days ago by ▴ 780 • written 18 days ago by • 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 5 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
0
votes
4
replies
255
views
Minfi - estimatecellscount
min minfi
updated 11 days ago by 65k • written 6 weeks ago by • 0
0
votes
0
replies
203
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
9 weeks ago Felix • 0
0
votes
1
reply
184
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
7
replies
470
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
2
replies
570
views
EPIC array hg38 annotation?
minfi DMRcate
3 months ago • updated 12 weeks ago mycetes • 0
0
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0
replies
268
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
3
votes
2
replies
471
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
5 months ago • updated 4 months ago kyj2226 • 0
0
votes
1
reply
335
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
5
replies
936
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
7 months ago • updated 6 months ago dorota.komar • 0
0
votes
2
replies
677
views
minfi differential methylation analysis errors
minfi
6 months ago matthew.sinton • 0
0
votes
3
replies
573
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
14
replies
2.0k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
402
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
953
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 12 months ago by ▴ 780 • written 12 months ago by ▴ 10
0
votes
2
replies
577
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 6 weeks ago by • 0 • written 12 months ago by • 0
0
votes
1
reply
547
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 13 months ago by 50k • written 13 months ago by • 0
0
votes
0
replies
414
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
13 months ago edward.esiribloom • 0
6
votes
5
replies
6.1k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 6 months ago by ▴ 10 • written 13 months ago by ▴ 50
0
votes
1
reply
617
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
4
replies
1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 14 months ago by 65k • written 14 months ago by • 0
1
vote
3
replies
848
views
Analysing Genome Studio .txt files with minfi
minfi
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 14 months ago by • 0
0
votes
1
reply
712
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
948
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
0
votes
1
reply
1.0k
views
minfi read.metharray.sheet error
minfi
updated 17 months ago by 65k • written 17 months ago by • 0
0
votes
1
reply
940
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
544
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
21 months ago calen.p.ryan • 0
0
votes
0
replies
714
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
23 months ago runye • 0
0
votes
1
reply
906
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
3
replies
1.2k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.1 years ago • updated 24 months ago ramonfallon ▴ 20
0
votes
2
replies
2.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 2.0 years ago by • 0 • written 8.6 years ago by ▴ 10
0
votes
0
replies
927
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.1 years ago octaviompa • 0
0
votes
0
replies
647
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago Rebecca • 0
0
votes
1
reply
841
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.2 years ago by • 0
0
votes
1
reply
887
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
744
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 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
0
replies
770
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3.0 years ago kyleyxw • 0
2
votes
2
replies
874
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
0
votes
0
replies
798
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl minfi
3.1 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 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
1
vote
5
replies
4.2k
views
minfi - error when reading idat files
minfi methylation
updated 20 months ago by • 0 • written 6.9 years ago by ▴ 10
0
votes
9
replies
2.8k
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 3.3 years ago by ★ 6.5k • written 3.3 years ago by ▴ 160
50 results • Page 1 of 1
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Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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