Showing : methylationarray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
10 months ago user_bioinfo • 0
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388
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
12 months ago charlie.wright • 0
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445
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 12 months ago by 68k • written 12 months ago by • 0
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2
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612
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
14 months ago Meghan • 0
2
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1
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922
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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 17 months ago by 68k • written 17 months ago by ▴ 20
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2
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1.3k
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
17 months ago ramiro.barrantes ▴ 10
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776
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 17 months ago by 68k • written 17 months ago by ▴ 10
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1
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945
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 17 months ago by 68k • written 17 months ago by • 0
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3
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1.1k
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 14 months ago by • 0 • written 17 months ago by ▴ 10
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2
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1.9k
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
updated 8 months ago by • 0 • written 19 months ago by • 0
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1
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1.0k
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 14 months ago by • 0 • written 19 months ago by • 0
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2
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2.5k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 21 months ago by ▴ 20 • written 21 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 20 months ago by 53k • written 21 months ago by • 0
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2
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2.9k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
21 months ago Yveto • 0
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0
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656
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
23 months ago Giovanni Calice ▴ 160
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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
23 months ago • updated 17 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 23 months ago by 53k • written 23 months ago by • 0
1
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7
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1.9k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 15 months ago by • 0 • written 23 months ago by • 0
1
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1
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1.8k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 24 months ago by 68k • written 24 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 2.0 years ago by 68k • written 2.0 years ago by • 0
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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
2.0 years 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
2.0 years ago mikat • 0
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1
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1.5k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
5
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5
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1.7k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.5 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 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
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6
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2.1k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.8 years ago by ▴ 230 • written 2.8 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 2.9 years ago by 53k • written 2.9 years ago by • 0
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4
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2.1k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
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5
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2.4k
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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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1.2k
views
Limma model orientation
limma methylation MethylationArray
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
2
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2
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2.1k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.9 years ago • updated 3.8 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
5.1 years ago epibio ▴ 10
6
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6
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2.7k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
5.1 years ago • updated 5.0 years ago MoltenLight ▴ 10
2
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7
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4.2k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.3 years ago by • 0 • written 5.2 years ago by ▴ 20
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0
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974
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.3 years ago coobzie • 0
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Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 160
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
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Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
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