Showing : MethylationArray • reset
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 5 days ago by 67k • written 5 days ago by • 0
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2
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336
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
9 weeks ago • updated 8 weeks ago Meghan • 0
2
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1
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398
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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 4 months ago by 67k • written 4 months ago by ▴ 10
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2
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581
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
4 months ago ramiro.barrantes ▴ 10
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350
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 4 months ago by 67k • written 4 months ago by ▴ 10
1
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1
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456
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 4 months ago by 67k • written 4 months ago by • 0
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3
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509
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
0
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2
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635
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
written 6 months ago by • 0
0
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1
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550
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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 weeks ago by • 0 • written 6 months ago by • 0
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2
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1.1k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
3
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2
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825
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 8 months ago by 52k • written 9 months ago by • 0
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2
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1.4k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
9 months ago Yveto • 0
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0
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430
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 months ago Giovanni Calice ▴ 160
1
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3
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1.6k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
11 months ago • updated 4 months ago s.malik • 0
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11
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1.3k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 months ago by 52k • written 11 months ago by • 0
1
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7
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1.2k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 3 months ago by • 0 • written 11 months ago by • 0
1
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1
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1.2k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 11 months ago by 67k • written 11 months ago by • 0
0
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7
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993
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error in reading idat files and creating rgset
minfi MethylationArray
updated 11 months ago by 67k • written 11 months ago by • 0
1
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2
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787
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 months ago mico • 0
1
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4
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1.1k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 months ago mikat • 0
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1
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1.1k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 16 months ago by 67k • written 16 months ago by • 0
5
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5
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1.2k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
17 months ago Jitendra ▴ 10
1
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1
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812
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
2
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6
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1.5k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 21 months ago by ▴ 200 • written 21 months ago by • 0
0
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1
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776
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 22 months ago by 52k • written 22 months ago by • 0
0
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4
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1.5k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 23 months ago by 67k • written 23 months ago by • 0
0
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5
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1.8k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 23 months ago by • 0
2
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1
reply
875
views
Limma model orientation
limma methylation MethylationArray
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
2
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2
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1.6k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.8 years ago fluentin44 • 0
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0
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1.2k
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.0 years ago epibio ▴ 10
6
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6
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2.0k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.0 years ago MoltenLight ▴ 10
2
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7
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3.1k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 15 months ago by • 0 • written 4.1 years ago by ▴ 20
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0
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767
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.2 years ago coobzie • 0
33 results • Page 1 of 1
Recent ...
Replies
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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