Showing : MethylationArray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
4 weeks ago user_bioinfo • 0
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236
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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 weeks ago charlie.wright • 0
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 3 months ago by 68k • written 3 months ago by • 0
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425
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
5 months ago Meghan • 0
2
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1
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546
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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 7 months ago by 68k • written 7 months ago by ▴ 20
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844
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
7 months ago ramiro.barrantes ▴ 10
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489
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 7 months ago by 68k • written 7 months ago by ▴ 10
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1
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620
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 7 months ago by 68k • written 7 months ago by • 0
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3
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675
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 4 months ago by • 0 • written 8 months ago by ▴ 10
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2
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759
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
written 9 months ago by • 0
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1
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717
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 5 months ago by • 0 • written 9 months ago by • 0
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2
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1.7k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 11 months ago by ▴ 20 • written 11 months ago by • 0
3
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2
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923
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 11 months ago by 52k • written 11 months ago by • 0
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2.0k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
12 months ago Yveto • 0
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
13 months ago Giovanni Calice ▴ 160
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3
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1.9k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
13 months ago • updated 7 months ago s.malik • 0
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11
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1.5k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 13 months ago by 52k • written 14 months ago by • 0
1
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7
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1.4k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 6 months ago by • 0 • written 14 months ago by • 0
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1
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1.4k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 14 months ago by 68k • written 14 months ago by • 0
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7
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1.1k
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error in reading idat files and creating rgset
minfi MethylationArray
updated 14 months ago by 68k • written 14 months ago by • 0
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2
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902
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
14 months ago mico • 0
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4
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1.3k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
14 months ago mikat • 0
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1
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1.2k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 18 months ago by 68k • written 18 months ago by • 0
5
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5
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1.3k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
20 months ago Jitendra ▴ 10
1
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1
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888
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 24 months ago by ▴ 40 • written 24 months ago by • 0
2
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6
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1.7k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.0 years ago by ▴ 230 • written 2.0 years ago by • 0
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1
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901
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
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4
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1.7k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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5
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2.0k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.1 years ago by • 0
2
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1
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943
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Limma model orientation
limma methylation MethylationArray
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
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2
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1.7k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.1 years ago • updated 3.0 years ago fluentin44 • 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
4.3 years ago epibio ▴ 10
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6
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2.1k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.3 years ago • updated 4.2 years ago MoltenLight ▴ 10
2
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7
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3.4k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 18 months ago by • 0 • written 4.4 years ago by ▴ 20
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814
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.5 years ago coobzie • 0
35 results • Page 1 of 1
Recent ...
Replies
Comment: Intepretation of results by Tom • 0
[Locksmith Wombwell][1] I have been interested in using AUCell as a way to determine significantly enriched pathways in my single cell spat…
Comment: Gene Ontology (GO) Analysis by Tom • 0
[Locksmith near me][1] Hello, I'm learning about Gene Ontology analysis. I'm trying to understand the difference between the hyperGTest fun…
Comment: DiffBind; Error: No sites have activity greater than filter value by etiennedanis • 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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