Showing : MethylationArray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
9 months ago user_bioinfo • 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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409
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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
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2
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593
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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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819
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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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734
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by ▴ 10
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1
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847
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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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967
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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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976
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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
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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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640
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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
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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
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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
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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 2.7 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
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.8 years ago by 68k • written 2.9 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
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1.1k
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
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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
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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
Recent ...
Replies
Answer: Confounded design, batch effect correction (edgeR) by nig.httopss • 0
To perform gene matching accurately, you should use the formula ~0 + Group + Batch in the design matrix to better manage sample groups. Sin…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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