Bioconductor Methylation

Showing : methylation • reset

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DMR Methylation R Gviz

updated 5 months ago by Robert Ivanek ▴ 730 • written 3.0 years ago by ltzhou • 0

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2.0k

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ChAMP methylation BMIQ

updated 5 months ago by peter.brederlo • 0 • written 5.0 years ago by moldach ▴ 20

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1.8k

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ChAMP champ methylation

updated 8 months ago by mike • 0 • written 4.1 years ago by jkong • 0

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282

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EPICV1 Methylation combineArrays minifi EPICv2manifest

4 weeks ago • updated 23 hours ago Kim • 0

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1.4k

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minfi software error methylation illumina450k

updated 11 months ago by kuzn.di • 0 • written 8.4 years ago by pm2015 • 0

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546

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edgeR methylation

updated 3 months ago by Gordon Smyth 50k • written 3 months ago by sat • 0

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159

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bsseq methylation

updated 4 weeks ago by James W. MacDonald 65k • written 4 weeks ago by ja569116 • 0

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256

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Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm

4 months ago kyj2226 • 0

8 results • Page 1 of 1

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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