DNA methylation data and P values

Question

[maryak]

I am new to dealing with DNA methylation data. I am unable to understand how to calculate P values .My problem is to distinguish between cancerous and non cancerous samples.

[Basti]

Which pipeline of DNA methylation analysis did you follow ?

[maryak]

sorry I don't know about pipeline. What do you mean by pipeline? i am using TCGA datasets

[Basti]

Which bioinformatic tool or packages are you using to perform your analysis ? Did you follow a specific tutorial ?

[maryak]

I am using TCGA datasets and R studio and Python as programming language .

[Basti]

You can follow some R tutorials that will help you to conduct a differential analysis, depending on the type of data you are analyzing :

• https://bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html
• Methylation Analysis Tutorial in R - Part 1
• https://compgenomr.github.io/book/data-filtering-and-exploratory-analysis.html#reading-methylation-call-files
• https://www.bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html