Showing : MethylationArray • reset
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
6 weeks ago • updated 28 days ago Giovanni Calice ▴ 160
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215
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 6 weeks ago by ▴ 40 • written 6 weeks ago by • 0
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11
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660
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
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139
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
7 weeks ago BioinfoMug • 0
1
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6
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428
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Library size normalization in methylation count analysis
edgeR MethylationArray
7 weeks ago mico • 0
1
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1
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246
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
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7
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402
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error in reading idat files and creating rgset
minfi MethylationArray
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
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2
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291
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
9 weeks ago mico • 0
1
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4
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411
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
10 weeks ago • updated 9 weeks ago mikat • 0
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1
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685
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 6 months ago by 65k • written 6 months ago by • 0
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763
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
1
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1
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536
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 11 months ago by ▴ 40 • written 11 months ago by • 0
2
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6
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1.0k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 11 months ago by ▴ 170 • written 11 months ago by • 0
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1
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521
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 12 months ago by 50k • written 12 months ago by • 0
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4
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981
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 13 months ago by 65k • written 13 months ago by • 0
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5
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1.2k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 13 months ago by • 0
2
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1
reply
640
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Limma model orientation
limma methylation MethylationArray
updated 23 months ago by 65k • written 23 months ago by • 0
2
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2
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1.2k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.0 years ago fluentin44 • 0
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0
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949
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.2 years ago epibio ▴ 10
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6
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1.5k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
3.3 years ago • updated 3.2 years ago MoltenLight ▴ 10
2
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7
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2.4k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 months ago by • 0 • written 3.3 years ago by ▴ 20
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0
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608
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.4 years ago coobzie • 0
22 results • Page 1 of 1
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Comment: flowStats Search Error by tholmes • 0
Thank you so much!
Comment: what is the sampleFiles by James W. MacDonald 65k
I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.
Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
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