I am a novice in the field of bioinformatics. I am currently trying to analyze the gene expression levels and DNA methylation levels for a gene of interest. I have retrieved the data from the TCGA Pancan dataset from XenaBrowser for all 33 cancer types. I want to compare the relative level of gene expression and DNA methylation for all cancers. For a preliminary data analysis, I used the 25th percentile cut-off: anything higher than the 25% cut-off was considered "high" gene expression and anything below the 25% cut-off was considered "low" gene expression. However, I am not sure there is the most soundway to do this analysis.
Are there any recommendations on how I can compare the relative levels of gene expression and DNA methylation for the 33 different cancer types?
