I am trying to compare the gene expression of a family of enzymes from both glioblastoma and low grade glioma databases from TCGA but I am not sure whether the data I get from CBioPortal is "ready" to analyze or requires some sort of log or exponential transformation. I downloaded U133 microarray data for glioblastoma and these values range between approximately 3-11. As for RNA-Seq data from low grade gliomas, I have a range of 0-2000. I did not find any information about how this data was treated aside from "mRNA z-Scores (U133 microarray only) compared to the expression distribution of each gene tumors that are diploid for this gene." and "(RNA Seq V2 RSEM) compared to the expression distribution of each gene tumors that are diploid for this gene."
Just to make it clear, I am not intending to compare microarray and RNA-seq data (I know it's not okay!). I intend to compare the expression of several genes across samples in both databases separately.