Showing : MethylationArray • reset
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267
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
9 months ago user_bioinfo • 0
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0
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374
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
11 months ago charlie.wright • 0
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411
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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 11 months ago by • 0
1
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2
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595
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
13 months ago Meghan • 0
2
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1
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825
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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 16 months ago by 68k • written 16 months ago by ▴ 20
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2
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1.2k
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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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1
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737
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by ▴ 10
1
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1
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857
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 16 months ago by 68k • written 16 months ago by • 0
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3
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970
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 13 months ago by • 0 • written 16 months ago by ▴ 10
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2
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1.8k
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
updated 7 months ago by • 0 • written 18 months ago by • 0
0
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1
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977
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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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2
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2.3k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 20 months ago by ▴ 20 • written 20 months ago by • 0
3
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2
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1.2k
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 19 months ago by 53k • written 20 months ago by • 0
1
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2
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2.6k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
20 months ago Yveto • 0
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0
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641
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
22 months ago Giovanni Calice ▴ 160
1
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3
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2.3k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
22 months ago • updated 16 months ago s.malik • 0
0
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11
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2.0k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 22 months ago by 53k • written 22 months ago by • 0
1
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7
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1.8k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 14 months ago by • 0 • written 22 months ago by • 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
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7
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1.4k
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error in reading idat files and creating rgset
minfi MethylationArray
updated 23 months ago by 68k • written 23 months ago by • 0
1
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2
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1.2k
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
23 months ago mico • 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
0
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1
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1.4k
views
EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
5
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5
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1.6k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.4 years ago Jitendra ▴ 10
1
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1
reply
1.1k
views
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
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1
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1.1k
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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
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4
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2.0k
views
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
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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
2
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1
reply
1.2k
views
Limma model orientation
limma methylation MethylationArray
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
2
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2
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2.0k
views
Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.8 years ago fluentin44 • 0
0
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0
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1.4k
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
5.0 years ago epibio ▴ 10
6
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6
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2.5k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray limma
5.0 years ago • updated 4.9 years ago MoltenLight ▴ 10
2
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7
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4.0k
views
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
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0
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960
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.2 years ago coobzie • 0
35 results • Page 1 of 1
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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results by sup0903 • 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
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