DNA methylation batch effect remove

DNA methylation batch effect remove

1

Hi,

I’m studying about DNA methylation.

I draw heatmap with beta-value, but there are batch effects..

How can I remove these cgID with studio R?enter image description here


DNA


effect


batch


methylation

• 24 views

Can you explain what do you mean by ‘beta-value’?

Generally batch effect could be removed by several filtering method, one of them is to filter through binomial test. Each CG called for methylation is based on read number and binomial could filter the probability of error of miscalled reads which support the methylation. In R you can use:

binom.test(x, n, p = 0.5,
alternative = c(“two.sided”, “less”, “greater”),
conf.level = 0.95)

Where n = your total reads mapped at particular CG and x = reads supporting methylated reads.

Before this binomial step, you can also filter each CG with a minimum number of reads mapped.

Also, before plotting such a huge heatmap I suggest you to plot the dendrogram tree and PCA on the sample/replicate basis. This could tell you how samples are associated or apart from each other. All these steps can be done in R or RStudio.

You can also follow R package MethylKit which has a dedicated step to remove experimental artifacts
bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html#34_Batch_effects


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