Showing : MethylationArray • reset
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160
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235
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 7 weeks ago by ▴ 40 • written 7 weeks ago by • 0
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700
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
8 weeks ago BioinfoMug • 0
1
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6
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451
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Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
1
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1
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269
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
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7
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425
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error in reading idat files and creating rgset
minfi MethylationArray
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
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304
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago mico • 0
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438
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 weeks ago mikat • 0
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716
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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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779
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
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1
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551
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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 12 months ago by • 0
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1.1k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 12 months ago by ▴ 170 • written 12 months ago by • 0
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 12 months ago by 50k • written 13 months ago by • 0
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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
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646
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Limma model orientation
limma methylation MethylationArray
updated 24 months ago by 65k • written 24 months ago by • 0
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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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957
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 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
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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 3.4 years ago by ▴ 20
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610
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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: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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