Bioconductor Methylation

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MethylationArray methylationArrayAnalysis MethylationArrayData meffil methylation

updated 10 hours ago by James W. MacDonald 65k • written 14 hours ago by kyj2226 • 0

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311

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EPICV1 Methylation combineArrays minifi EPICv2manifest

4 weeks ago • updated 4 days ago Kim • 0

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163

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bsseq methylation

updated 5 weeks ago by James W. MacDonald 65k • written 5 weeks ago by ja569116 • 0

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551

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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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263

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Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm

4 months ago kyj2226 • 0

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1.4k

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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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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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2.0k

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ChAMP methylation BMIQ

updated 6 months ago by peter.brederlo • 0 • written 5.0 years ago by moldach ▴ 20

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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

9 results • Page 1 of 1

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Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k

Regardless of whether it agrees with `t.test` or not, the formula given in the original question is correct and yours is not. Your formula …

Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by nbay13 • 0

A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…

Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k

sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…

Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k

I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?

Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k

If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…

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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu

Answer: Extremely small p-values using Limma for proteomic data

Answer: How to save the DEXSeq results

Answer: minfi support of illumina Infinium methylationEPIC v2.0

Comment: minfi support of illumina Infinium methylationEPIC v2.0

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