Differential methylation analysis

Question

[David_emir]

Hello All,

I am currently working on to understand the Methylation mechanism in Cancer condition. my area of study revolves around the mostly wet lab and I have basic knowledge about coding, here I need your help. I have two sets of samples from TCGA LUSC and LUAD samples. I want to do Differential methylation analysis between LUSC cancer cells Vs. LUAD cancer cells. Please note I don't want a methylation analysis b/w Normal Vs Tumor. I have tried using TCGAbiolinks but it's not allowing me to choose samples, it's forcing me to have a DME analysis b/w Normal samples VS LUSC or Normal Vs LUAD. Can you please let me know how to solve this issue. Please let me know how to make TCGABiolinks package to understand that I need a comparison b/w samples which I have defined. Sorry for this lengthy post.But trust me this is my last stop. Before I abandon this task.

Thanks in advance,
Dave.

[WouterDeCoster]

Please select a more appropriate title for your thread. "Differential gene expression Analysis" --> you are talking about differential methylation analysis? I would suggest: "differential methylation analysis TCGA LUSC vs TCGA LUAD" to be more specific.

You may have to download the data and process it yourself.

[David_emir]

Sorry for that. I have rectified it. Can you please let me know how to go about this?

[WouterDeCoster]

I wouldn't know, but it looks like this bioconductor package has both methods for downloading data and analysis: TCGA Workflow

Answer 1

[Mathias]

If you have already downloaded your data, you can also make use of the ChAMP package. https://bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html It makes use of the limma package, so you'd use linear models instead of regular t-tests to find DMPs.

This section show you how you can specify your own groups in the pd file; so you can run an analysis between 2 tumor samples if you wish.

It also offers some visualization for quality control, although you'd lose the automatic volcano plot generation.