Bioconductor MethylationArray

Showing : MethylationArray • reset

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309

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linearregression epicarray MethylationArray limma

5 weeks ago Jitendra ▴ 10

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309

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methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray

updated 4 months ago by belinda.phipson ▴ 40 • written 4 months ago by Grace • 0

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577

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DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray

updated 5 months ago by Tim Peters ▴ 140 • written 5 months ago by Grace • 0

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225

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methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray

updated 5 months ago by Gordon Smyth 48k • written 5 months ago by Grace • 0

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463

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methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray

updated 6 months ago by James W. MacDonald 63k • written 6 months ago by Grace • 0

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486

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methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray

written 6 months ago by Grace • 0

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461

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limma methylation MethylationArray

updated 16 months ago by James W. MacDonald 63k • written 17 months ago by fluentin44 • 0

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limma MethylationArrayData MethylationArray

17 months ago fluentin44 • 0

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747

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sva limma methylation MethylationArray

2.7 years ago epibio ▴ 10

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1.2k

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MethylationArray limma

2.7 years ago • updated 2.6 years ago MoltenLight ▴ 10

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1.9k

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MethylationArray methylationArrayAnalysis ChAMP

updated 18 months ago by l.milicic • 0 • written 2.8 years ago by Ankit ▴ 20

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477

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GeneExpression methyAnalysis MethylationArray

2.9 years ago coobzie • 0

12 results • Page 1 of 1

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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

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batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Answer: Batch correction and repeated measures

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