Showing : MethylationArray • reset
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
10 months ago user_bioinfo • 0
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383
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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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440
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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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609
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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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908
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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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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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769
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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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929
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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 7 months ago by • 0 • written 18 months ago by • 0
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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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2.8k
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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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650
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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 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 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 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 24 months ago by 68k • written 24 months 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 2.3 years ago by 68k • written 2.3 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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1.1k
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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
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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
3.8 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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2.6k
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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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972
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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
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Comment: Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics by mudasarnaeem2020 • 0
Promoting UDISE+ Features on Social Media to Increase Awareness https://udisseplus.com/[enter link description here][1] [1]: https://ud…
Comment: DiffBind plot.profile error by a2sahaaaq2c • 0
To resolve technical errors like installation failures or login issues, first ensure your device allows in the security settings and that…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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