Showing : MethylationArray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
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360
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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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378
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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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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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764
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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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715
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 15 months ago by 68k • written 15 months ago by ▴ 10
1
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1
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821
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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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924
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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
0
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1
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953
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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
1
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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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625
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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
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 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 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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1.2k
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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
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
views
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
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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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
reply
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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3.9k
views
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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946
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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: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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 …
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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