Bioconductor DNA methylation

Showing : DNA methylation • reset

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1.1k

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minfi cell proportion estimateCellCounts DNA Methylation

4.7 years ago grayapply2009 • 0

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2.3k

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normalization DNA methylation WGCNA

updated 5.5 years ago by Peter Langfelder ★ 3.0k • written 5.5 years ago by enora.fremy • 0

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1.2k

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medips medip-seq dna methylation dmr analysis

updated 6.1 years ago by Lukas Chavez ▴ 570 • written 6.1 years ago by mtefit • 0

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1.8k

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R gdc rna-seq dna methylation

updated 6.2 years ago by Sean Davis 21k • written 6.2 years ago by RichardJActon ▴ 50

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1.4k

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minfi normalization outliers dna methylation densityplot

6.4 years ago peter.fransquet • 0

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878

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differential variability dna methylation iEVORA DVP

6.6 years ago poojitha.stemcell ▴ 10

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1.2k

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rnbeads methylation methylationepic dna methylation

6.8 years ago gabrielrfries • 0

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1.3k

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dna methylation biseq

updated 7.0 years ago by Gordon Smyth 52k • written 7.0 years ago by ahmad.moousavi • 0

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2.1k

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tcgabiolinks dna methylation

updated 7.1 years ago by Marcel Ramos 700 • written 7.1 years ago by michaelwxf2012 • 0

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1.9k

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dna methylation illimina 450k methylation beta M significance

updated 7.2 years ago by James W. MacDonald 67k • written 7.2 years ago by skids121 • 0

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1.4k

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CNV minfi preprocessing dna methylation

7.7 years ago Thomas • 0

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1.1k

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microarray HM450 dna methylation cohcap

updated 7.9 years ago by James W. MacDonald 67k • written 7.9 years ago by poojitha.stemcell ▴ 10

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1.3k

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minfi bumphunter DNA methylation illumina450k

updated 8.5 years ago by James W. MacDonald 67k • written 8.5 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k

Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…

Votes

Answer: nightmare to make custom txdb for genomes from ToxoDB

Comment: nightmare to make custom txdb for genomes from ToxoDB

Answer: Normalizing batch effects using technical replicates for DGE analysis between tw

Answer: nightmare to make custom txdb for genomes from ToxoDB

A: Advice on correcting for batch effect using DESeq2

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