How can I analyze microarray and RNA-Seq data from TCGA?

Question

[rafaelpasc96]

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.

Answer 1

[Gema Sanz]

You can work directly with the data from cBioPortal, they provide microarray data as z-scores, which is normalized expression data (is the number of standard deviations from the mean a data point is). You can use it directly with the tools provided in cBioPortal or download it to do your own heatmaps, analysis, etc.

I think this is already answered here TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?