Showing : methylationArrayAnalysis • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 4 months ago by 68k • written 4 months ago by • 0
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
4 months ago user_bioinfo • 0
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2
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437
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 5 months ago by 68k • written 5 months ago by • 0
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
6 months ago a.alkema • 0
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294
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 6 months ago by 68k • written 6 months ago by • 0
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 11 months ago by ▴ 20 • written 11 months ago by ▴ 10
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
11 months ago ramiro.barrantes ▴ 10
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610
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 11 months ago by 68k • written 11 months ago by ▴ 10
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844
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 8 months ago by • 0 • written 13 months ago by • 0
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2.2k
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
16 months ago hortense96 • 0
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1.6k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 18 months ago by 68k • written 18 months ago by • 0
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
18 months ago mikat • 0
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 20 months ago by 52k • written 20 months ago by • 0
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6
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1.5k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
21 months ago aldea85 • 0
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1.3k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 22 months ago by 68k • written 22 months ago by • 0
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1.2k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 24 months ago by 68k • written 2.0 years ago by • 0
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3.9k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by ▴ 20
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.1 years ago Krzysztof • 0
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.2 years ago Irene • 0
1
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1
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985
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.3 years ago by ▴ 40 • written 2.3 years ago by • 0
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6
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1.8k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.3 years ago by ▴ 230 • written 2.3 years ago by • 0
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1.7k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.3 years ago arisarkar88 ▴ 40
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983
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
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1.0k
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
5
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2.4k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 25 days ago by • 0 • written 2.4 years ago by ▴ 80
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4
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1.8k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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5
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2.2k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.5 years ago by • 0
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1
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1.1k
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.7 years ago by ★ 2.0k
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3
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4.4k
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 2.1 years ago by • 0 • written 2.8 years ago by • 0
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7
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3.7k
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ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 2.8 years ago by 68k • written 3.3 years ago by • 0
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.4 years ago Jitendra ▴ 10
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1.3k
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getsex function error.
QualityControl methylationArrayAnalysis
3.5 years ago zusman • 0
2
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4
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1.9k
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How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis illuminaio beadarray DSS bsseqData
3.5 years ago Jojo • 0
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6
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4.7k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.1 years ago FWNL15 • 0
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2
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1.3k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
4.4 years ago Kesava • 0
1
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8
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2.0k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
4.4 years ago chay • 0
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2
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1.8k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
4.4 years ago arisarkar88 ▴ 40
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2
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1.3k
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.5 years ago sissialva21 • 0
2
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7
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3.6k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 22 months ago by • 0 • written 4.7 years ago by ▴ 20
1
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1
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1.6k
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Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
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Comment: EuroBioC2024 abstract submission is open! by rajilrfaze • 0
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Comment: p-adjusted values in multiple comparisons by ocanorocabayera • 0
Thank you Gordon for your thorough reply. It seems when MDS-plotting the obtained object from 'voom', that the points do not cluster togeth…
Comment: Are voomByGroup and voomLmFit compatible? by Gordon Smyth 52k
Not sure what "points" you are referring to, or what you mean by them being "weighted".
Answer: p-adjusted values in multiple comparisons by Gordon Smyth 52k
If your data was completely random, with no truly differentially expressed (DE) genes, then you would expect to get nearly 5% of the p-valu…
Answer: Are voomByGroup and voomLmFit compatible? by Gordon Smyth 52k
voomByGroup isn't part of Bioconductor, so questions about it should be send to the voomByGroup issues page. I haven't brought voomByGroup…
Votes
Answer: p-adjusted values in multiple comparisons
Comment: Very different log2 Fold changes with DESeq2 and explict calculation
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: Very different log2 Fold changes with DESeq2 and explict calculation
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