TXT or IDAT format for differential DNA Methylation analysis

Question

[ananta.kapoor]

I have to replicate the analysis in this paper- Genome-Wide Identification and Analysis of the Methylation of lncRNAs and Prognostic Implications in the Glioma I would really appreciate some help in the process. As it is a 3 year old paper I am going to the sites mentioned in the paper and collecting the current data. They had taken data from TCGA and TANRIC. They downloaded the TCGA Data through GDC Data portal, after applying filters mentioned in the paper there are DNA Methylation files with txt and idat formats which files to use for differential methylation analysis? txt has beta values idat has masked intensities.

Answer 1

[Hamid Ghaedi]

For differential methylation analysis, you would need M-value which is derived from beta-value. Now the question is should you proceed with the given beta values (as provided in the txt file) or do you need to generate the beta value yourself by analyzing idat files? If you do not have any plan to modify the TCGA pipeline for methylation analysis, or do the analysis from scratch, you may use provided beta-value