I am trying to do a rough analysis of a certain gene in various cancer types using data I downloaded from TCGA through Wanderer (http://gattaca.imppc.org:3838/wanderer/). The RNA seq data is provided as log2RPKM values. What I want to do is, for my gene of interest, pair up the RPKM values of normal and tumor samples from the same patient and use a simple test (for example, fold change >=|2|) to determine if the gene is upregulated, downregulated, or unchanged in each individual patient. The problem is that I have done some reading and am confused on whether this type of analysis makes sense with RPKM values. I am completely new to TCGA/bioinformatics so any advice is greatly appreciated!
Thanks very much in advance.