Showing : methylationarray • reset
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
3 days ago charlie.wright • 0
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 18 days ago by 68k • written 18 days ago by • 0
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344
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
11 weeks ago • updated 10 weeks ago Meghan • 0
2
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1
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418
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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 5 months ago by 68k • written 5 months ago by ▴ 10
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
5 months ago ramiro.barrantes ▴ 10
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 5 months ago by 68k • written 5 months ago by ▴ 10
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1
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471
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 5 months ago by 68k • written 5 months ago by • 0
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3
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544
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 10 weeks ago by • 0 • written 5 months ago by ▴ 10
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2
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662
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
written 6 months ago by • 0
0
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1
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571
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 10 weeks ago by • 0 • written 7 months ago by • 0
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1.2k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 9 months ago by ▴ 20 • written 9 months ago by • 0
3
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2
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842
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 8 months ago by 52k • written 9 months ago by • 0
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1.5k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
9 months ago Yveto • 0
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0
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 months ago • updated 10 months ago Giovanni Calice ▴ 160
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3
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1.6k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
11 months ago • updated 4 months ago s.malik • 0
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11
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1.3k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 months ago by 52k • written 11 months ago by • 0
1
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7
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1.2k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 3 months ago by • 0 • written 11 months ago by • 0
1
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1
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1.2k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 11 months ago by 68k • written 11 months ago by • 0
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7
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1.0k
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error in reading idat files and creating rgset
minfi MethylationArray
updated 12 months ago by 68k • written 12 months ago by • 0
1
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2
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801
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
12 months ago mico • 0
1
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4
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1.2k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
12 months ago mikat • 0
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1
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1.1k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by • 0
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5
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1.2k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
18 months ago Jitendra ▴ 10
1
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1
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818
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
2
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6
replies
1.5k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 21 months ago by ▴ 200 • written 21 months ago by • 0
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1
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801
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 22 months ago by 52k • written 22 months ago by • 0
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4
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1.5k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 23 months ago by 68k • written 23 months ago by • 0
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5
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1.8k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 23 months ago by • 0
2
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1
reply
886
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Limma model orientation
limma methylation MethylationArray
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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2
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1.6k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.8 years ago fluentin44 • 0
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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
4.1 years ago epibio ▴ 10
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6
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2.0k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.1 years ago • updated 4.0 years ago MoltenLight ▴ 10
2
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7
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3.2k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 16 months ago by • 0 • written 4.2 years ago by ▴ 20
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773
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.2 years ago coobzie • 0
34 results • Page 1 of 1
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Comment: DESeq2 adujsted p-value cutoff seemingly not working by Guilherme • 0
Thank you for your answer So the proper way to conduct the analysis is to put the filters in the results() function and later filter the da…
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp by Ian D. ▴ 70
Please can you comment on this @rory.
Comment: Why the order of sample names in the beta matrix affect the analysis results of by 81becky • 0
It sounds like you're experiencing a common issue with data alignment in Champ.DMP. Ensure that your beta matrix and PD files are consisten…
Comment: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by Blair • 0
@[Sprunki][1] wrote: Please read the vignette and think about adhering to the author's best practice, which discusses batch impacts. [1…
Comment: error in ChAMP loading file by 81becky • 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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