how to merge the DNA_methylation data downloaded for GDC database

Question

[fuzerxzzy]

I have downloaded the TCGA DNA methylation data by gdc_glient. The data is too large, and I have no idea how to deal with. There are more than 300 files, including .txt data. I hope to use ChAMP R package to analysis these，but I think first I should prepare the data to import into R. ChAMP only allow the .idat file, and I didn't find any other tutorial that it can import .txt data into R software. If you see this problem and you can solve it, hoping you can leave a message to help me. Thank you!

Answer 1

[Kevin Blighe]

ChAMP does not necessarily have to read iDAT files. Please check the vignette and documentation for the program. Essentially, the starting point is:

champ.process(fromIDAT = FALSE, ...)

I have processed methylation data from the TCGA and one does not even require ChAMP. You could simply read in all files and merge into a single data matrix of methylation beta (β) values. Then, your statistical comparisons would involve a Wilcoxon Signed Rank test between your groups of interest. You should add a 'difference in mean methylation' between each group as an extra cut-off, too (for example, mean(tumour) - mean(normal)).

Kevin

[fuzerxzzy]

I apologize for not replying earlier. Thank you for your response!

[Kevin Blighe]

No problem. I have already been to Mars and back since I posted my answer :)