TCGA methylation data analysis

Question

[dilrajkaur766]

Hi,

I have TCGA -HNSC Level3 methylation 450k dataset. Now I have to find Differential methylated regions between primary tumor and Sold tissue normal. I have explored some tools but they required IdAT files, is there any easy way to get IDAT files?

Also how to work with normalised Beta matrix (probes, beta value )across samples with Champ?

Any suggestion would be helpful.

Thank you

[Basti]

.idat files are available here

From the ChAMP pipeline : "As long as you have a methylation beta matrix and the corresponding phenotypes (pd) file, you can conduct nearly all of the ChAMP analysis. " So you can use the beta matrix, just follow the pipeline

Answer 1

[Zhenyu Zhang]

Where did you get your beta values? both beta values and idat should be available from the GDC.