Showing : minfi • reset
2
votes
1
reply
131
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 6 days ago by 65k • written 6 days ago by • 0
0
votes
4
replies
256
views
Minfi - estimatecellscount
min minfi
updated 14 days ago by 65k • written 6 weeks ago by • 0
1
vote
4
replies
216
views
minfi::read.metharray.exp
minfiData minfi
updated 19 days ago by ▴ 780 • written 21 days ago by • 0
2
votes
6
replies
1.5k
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
2
replies
579
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 7 weeks ago by • 0 • written 12 months ago by • 0
0
votes
0
replies
208
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
188
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
477
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 12 weeks ago by 65k • written 3 months ago by • 0
0
votes
2
replies
577
views
EPIC array hg38 annotation?
minfi DMRcate
3 months ago mycetes • 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
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
0
votes
0
replies
269
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
4 months ago kyj2226 • 0
3
votes
2
replies
472
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
5 months ago kyj2226 • 0
0
votes
1
reply
338
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 5 months ago by ▴ 780 • written 5 months ago by • 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 14 months ago by ▴ 50
0
votes
5
replies
948
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
682
views
minfi differential methylation analysis errors
minfi
7 months ago matthew.sinton • 0
0
votes
3
replies
578
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
1
reply
404
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 8 months ago by 65k • written 8 months 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
2
replies
1.4k
views
Error processing Infinium 450K Methylation data using Minfi
minfi software error methylation illumina450k
updated 12 months ago by • 0 • written 8.4 years ago by • 0
0
votes
3
replies
959
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
1
vote
8
replies
3.3k
views
Normalization starting from beta values in minfi
methylation minfi
written 8.0 years ago by ▴ 290
0
votes
1
reply
550
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
416
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
13 months ago edward.esiribloom • 0
0
votes
1
reply
622
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
3
votes
6
replies
2.1k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 14 months ago by • 0 • written 8.8 years ago by ▴ 370
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
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
6
votes
3
replies
9.9k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 14 months ago by • 0 • written 4.8 years ago by ▴ 10
1
vote
3
replies
851
views
Analysing Genome Studio .txt files with minfi
minfi
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
1
reply
715
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
951
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
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
1
reply
942
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 21 months ago by 65k • written 21 months ago by • 0
0
votes
0
replies
546
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
2
replies
1.2k
views
Error in read.metharray.exp
minfi epic microarray bioconductor
updated 22 months ago by • 0 • written 6.2 years ago by • 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
911
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
934
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.1 years ago octaviompa • 0
0
votes
0
replies
648
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago Rebecca • 0
0
votes
1
reply
845
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
1
reply
890
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
746
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
2.8 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
771
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3.0 years ago kyleyxw • 0
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
50 results • Page 1 of 1
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Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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