Showing : MethylationArray • reset
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
8 weeks ago • updated 7 weeks ago Meghan • 0
2
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1
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387
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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
1
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2
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562
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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
0
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1
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343
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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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440
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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
0
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3
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502
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 7 weeks ago by • 0 • written 4 months ago by ▴ 10
0
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2
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626
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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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534
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 7 weeks ago by • 0 • written 6 months ago by • 0
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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810
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 7 months ago by 52k • written 8 months ago by • 0
1
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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
8 months ago Yveto • 0
0
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0
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420
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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
10 months ago • updated 4 months ago s.malik • 0
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 10 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 12 weeks ago by • 0 • written 10 months ago by • 0
1
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1
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1.1k
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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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983
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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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782
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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
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 months ago mikat • 0
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 15 months ago by 67k • written 15 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
reply
806
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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
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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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768
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 21 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 22 months ago by 67k • written 22 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 22 months ago by • 0
2
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1
reply
869
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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
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
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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
0
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0
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764
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.2 years ago coobzie • 0
32 results • Page 1 of 1
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Answer: Problems with GSEA by Guido Hooiveld ★ 4.1k
The error `Duplicate values in names(stats) not allowed` (from `fgsea` that is used under the hood) shows that the input is not unique; in …
Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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