Showing : minfi • reset
0
votes
3
replies
988
views
Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 5 months ago by • 0 • written 7 months ago by • 0
1
vote
2
replies
792
views
normalizatino of dna methylation EPIC data
DNA minfiData minfiDataEPIC DNAMethylation minfi
8 months ago user_bioinfo • 0
4
votes
8
replies
1.8k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
11 months ago • updated 8 months ago xiaofeiwang198266 • 0
1
vote
4
replies
948
views
Handling Epic Array Data
minfi
11 months ago Melisa Tecik • 0
2
votes
2
replies
756
views
preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
11 months ago Rakesh • 0
2
votes
5
replies
1.0k
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
993
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 14 months ago by • 0 • written 14 months ago by • 0
4
votes
12
replies
5.7k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 15 months ago by ▴ 230 • written 23 months ago by ▴ 20
0
votes
1
reply
733
views
minfi - bumphunter value problem
bumphunter minfiData minfi bumphun
updated 15 months ago by 68k • written 16 months ago by • 0
0
votes
0
replies
694
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
16 months ago pcibin • 0
0
votes
2
replies
1.2k
views
Epicv2 conversion fail
minfi
16 months ago Alex • 0
2
votes
4
replies
3.2k
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 4 months ago by • 0 • written 18 months ago by • 0
1
vote
4
replies
892
views
minfi::read.metharray.exp
minfiData minfi
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
0
votes
4
replies
1.0k
views
Minfi - estimatecellscount
min minfi
updated 18 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
768
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
20 months ago Felix • 0
0
votes
1
reply
653
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
7
replies
1.4k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
3.0k
views
EPIC array hg38 annotation?
minfi DMRcate
21 months ago mycetes • 0
0
votes
0
replies
1.2k
views
Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
22 months ago kyj2226 • 0
3
votes
2
replies
1.3k
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE CpG minfi CpGinterrogation
23 months ago kyj2226 • 0
0
votes
1
reply
892
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
votes
5
replies
1.8k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.1 years ago dorota.komar • 0
0
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2
replies
1.5k
views
minfi differential methylation analysis errors
minfi
2.1 years ago matthew.sinton • 0
0
votes
3
replies
1.4k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
votes
14
replies
4.5k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 21 months ago by • 0 • written 2.2 years ago by • 0
1
vote
2
replies
1.5k
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 4 months ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
3
replies
1.8k
views
Batch correction using control probes in EPIC array data
RnBeads minfiData minfi EPICarray
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by ▴ 10
0
votes
2
replies
1.1k
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 19 months ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
0
replies
774
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
2.6 years ago edward.esiribloom • 0
6
votes
6
replies
10k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0 minfi
updated 13 months ago by • 0 • written 2.6 years ago by ▴ 50
0
votes
1
reply
1.1k
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.6 years ago by 68k • written 2.7 years ago by • 0
0
votes
4
replies
1.9k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
3
replies
1.7k
views
Analysing Genome Studio .txt files with minfi
minfi
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
5
replies
2.3k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.7 years ago by • 0
0
votes
1
reply
1.4k
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic read.metharray.sheet list.files minfi
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
3
replies
2.0k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
0
votes
1
reply
1.6k
views
minfi read.metharray.sheet error
minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
1
reply
1.8k
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
0
replies
979
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
3.2 years ago calen.p.ryan • 0
0
votes
0
replies
1.1k
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
3.4 years ago runye • 0
0
votes
1
reply
1.5k
views
what is the format of DMPfinder in minfi package
minfi
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
3
replies
1.8k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.6 years ago • updated 3.5 years ago ramonfallon ▴ 20
0
votes
2
replies
3.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19 minfi illuminahumanmethylation450k.db methylation
updated 3.5 years ago by • 0 • written 10.1 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.5 years ago octaviompa • 0
0
votes
0
replies
931
views
Minfi package: controlStripPlot colors
minfi
3.7 years ago Rebecca • 0
0
votes
1
reply
1.4k
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 failingprobes detectionP minfi
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
9
replies
4.3k
views
clarification about bumphunter value output
minfi bumphunter
updated 2.4 years ago by • 0 • written 7.7 years ago by • 0
0
votes
1
reply
1.4k
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 4.1 years ago by ▴ 780 • written 4.1 years ago by • 0
0
votes
0
replies
1.2k
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.2 years ago ponche_de_kiwi • 0
281 results • Page 1 of 6
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Comment: After running samtools, the featureCounts command crashed. by eja.gssssse.r.m • 0
The buffer overflow detected error in your featureCount step usually indicates that the program is trying to write more data into memory …
Comment: gene Set with high AUC score but no cells assigned to cell type by eja.gssssse.r.m • 0
It sounds like your AUCell results may be showing high AUC scores without cell assignment due to thresholding or scoring cutoffs. Think of …
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Comment: Integration: Paired-end vs healthy single-end from a different source by igkryycpinmshzugby • 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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