Showing : MethylationArray • reset
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
25 days ago • updated 24 days ago Meghan • 0
2
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1
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359
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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 3 months ago by 67k • written 3 months ago by ▴ 10
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509
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
3 months ago ramiro.barrantes ▴ 10
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1
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301
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 3 months ago by 67k • written 3 months ago by ▴ 10
1
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1
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405
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 3 months ago by 67k • written 3 months ago by • 0
0
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3
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457
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 18 days ago by • 0 • written 3 months ago by ▴ 10
0
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2
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603
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
written 5 months ago by • 0
0
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1
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492
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 24 days ago by • 0 • written 5 months ago by • 0
0
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2
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990
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 7 months ago by ▴ 20 • written 7 months ago by • 0
3
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2
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787
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 6 months ago by 52k • written 7 months ago by • 0
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2
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1.3k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
7 months ago Yveto • 0
0
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0
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399
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
9 months ago Giovanni Calice ▴ 160
1
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3
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1.5k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
9 months ago • updated 3 months ago s.malik • 0
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 9 months ago by 52k • written 9 months ago by • 0
1
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7
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1.1k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 8 weeks ago by • 0 • written 9 months ago by • 0
1
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1
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1.0k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 10 months ago by 67k • written 10 months ago by • 0
0
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7
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944
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error in reading idat files and creating rgset
minfi MethylationArray
updated 10 months ago by 67k • written 10 months ago by • 0
1
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2
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752
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
10 months ago mico • 0
1
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4
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1.0k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
10 months ago mikat • 0
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 14 months ago by 67k • written 14 months ago by • 0
5
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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
16 months ago Jitendra ▴ 10
1
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1
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788
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 19 months ago by ▴ 40 • written 20 months ago by • 0
2
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6
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1.5k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 20 months ago by ▴ 200 • written 20 months ago by • 0
0
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1
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746
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 20 months ago by 52k • written 21 months ago by • 0
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 21 months ago by 67k • written 21 months ago by • 0
0
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5
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1.7k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 21 months ago by • 0
2
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1
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855
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Limma model orientation
limma methylation MethylationArray
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
2
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2
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1.6k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.7 years ago fluentin44 • 0
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0
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1.1k
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.9 years ago epibio ▴ 10
6
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6
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1.9k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
3.9 years ago MoltenLight ▴ 10
2
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7
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3.0k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 14 months ago by • 0 • written 4.0 years ago by ▴ 20
0
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0
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753
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.1 years ago coobzie • 0
32 results • Page 1 of 1
Recent ...
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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