Showing : MethylationArray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
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358
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
10 months ago charlie.wright • 0
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377
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 10 months ago by 68k • written 10 months ago by • 0
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2
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571
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
12 months ago Meghan • 0
2
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1
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751
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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 15 months ago by 68k • written 15 months ago by ▴ 20
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2
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1.1k
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
15 months ago ramiro.barrantes ▴ 10
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709
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 15 months ago by 68k • written 15 months ago by ▴ 10
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1
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818
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 15 months ago by 68k • written 15 months ago by • 0
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3
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919
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 12 months ago by • 0 • written 15 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 6 months ago by • 0 • written 17 months ago by • 0
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1
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945
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 12 months ago by • 0 • written 17 months ago by • 0
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2
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2.2k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 19 months ago by ▴ 20 • written 19 months ago by • 0
3
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2
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1.1k
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 18 months ago by 53k • written 19 months ago by • 0
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2
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2.5k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
19 months ago Yveto • 0
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0
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622
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
21 months ago Giovanni Calice ▴ 160
1
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3
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2.2k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
21 months ago • updated 15 months ago s.malik • 0
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11
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1.9k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 21 months ago by 53k • written 21 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 13 months ago by • 0 • written 21 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 22 months ago by 68k • written 22 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 22 months ago by 68k • written 22 months ago by • 0
1
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2
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1.1k
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
22 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
22 months ago mikat • 0
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1
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1.4k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
5
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5
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1.6k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.3 years ago Jitendra ▴ 10
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 2.6 years ago by ▴ 40 • written 2.6 years ago by • 0
2
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6
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2.0k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 230 • written 2.6 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 2.7 years ago by 53k • written 2.7 years ago by • 0
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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 2.8 years ago by 68k • written 2.8 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 2.8 years ago by • 0
2
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1
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1.1k
views
Limma model orientation
limma methylation MethylationArray
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
2
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2
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2.0k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.7 years ago fluentin44 • 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
4.9 years ago epibio ▴ 10
6
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6
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2.4k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.9 years ago MoltenLight ▴ 10
2
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7
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3.8k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.2 years ago by • 0 • written 5.0 years ago by ▴ 20
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0
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944
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.1 years ago coobzie • 0
35 results • Page 1 of 1
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Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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