Showing : methylationarrayanalysis • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 9 months ago by 68k • written 9 months ago by • 0
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267
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
9 months ago user_bioinfo • 0
0
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2
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787
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 10 months ago by 68k • written 10 months ago by • 0
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2
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600
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
11 months ago a.alkema • 0
0
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413
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 11 months ago by 68k • written 12 months ago by • 0
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13
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2.3k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 16 months ago by ▴ 20 • written 16 months ago by ▴ 10
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
16 months ago ramiro.barrantes ▴ 10
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739
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by ▴ 10
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982
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 13 months ago by • 0 • written 18 months ago by • 0
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7
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2.5k
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
21 months ago hortense96 • 0
1
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1
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1.7k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 23 months ago by 68k • written 23 months ago by • 0
1
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4
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1.7k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
23 months ago mikat • 0
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4
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1.9k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
3
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6
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1.7k
views
Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.2 years ago aldea85 • 0
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1.4k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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3
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1.4k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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1
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4.0k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
1
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2
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1.2k
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.5 years ago Krzysztof • 0
1
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2
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1.5k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.6 years ago Irene • 0
1
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1
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1.1k
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
2
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6
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2.0k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.7 years ago by ▴ 230 • written 2.7 years ago by • 0
0
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2
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1.8k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.7 years ago arisarkar88 ▴ 40
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1
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1.1k
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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1
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1.1k
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
5
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2
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2.6k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 5 months ago by • 0 • written 2.9 years ago by ▴ 80
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4
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2.0k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
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5
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2.3k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.9 years ago by • 0
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 3.1 years ago by ★ 2.0k
0
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3
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4.7k
views
Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 2.5 years ago by • 0 • written 3.2 years ago by • 0
0
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7
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4.0k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 3.2 years ago by 68k • written 3.7 years ago by • 0
0
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0
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1.1k
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.8 years ago Jitendra ▴ 10
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0
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1.4k
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getsex function error.
QualityControl methylationArrayAnalysis
3.9 years ago zusman • 0
2
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4
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2.0k
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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
4.0 years ago Jojo • 0
0
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6
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4.9k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.5 years ago FWNL15 • 0
0
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2
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1.4k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
4.8 years ago Kesava • 0
1
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8
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2.2k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
4.8 years ago chay • 0
0
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2
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2.0k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
4.8 years ago arisarkar88 ▴ 40
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2
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1.4k
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
5.0 years ago sissialva21 • 0
2
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7
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4.0k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.3 years ago by • 0 • written 5.1 years ago by ▴ 20
1
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1
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1.8k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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