Showing : MethylationArray • reset
6
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
3.3 years ago • updated 3.2 years ago MoltenLight ▴ 10
5
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5
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766
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
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
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
2
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642
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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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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
1
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6
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430
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Library size normalization in methylation count analysis
edgeR MethylationArray
7 weeks ago mico • 0
1
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4
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413
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
10 weeks ago mikat • 0
1
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2
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292
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
10 weeks ago mico • 0
1
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0
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142
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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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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
1
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1
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250
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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 8 weeks ago by • 0
0
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0
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131
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
6 weeks ago • updated 29 days ago Giovanni Calice ▴ 160
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
0
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1
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216
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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
0
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1
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688
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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
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
0
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1
reply
525
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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
0
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4
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985
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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
0
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7
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406
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error in reading idat files and creating rgset
minfi MethylationArray
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
0
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11
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667
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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
0
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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: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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