5.7 years ago by
Memorial Sloan Kettering, New York, USA
Normalization happens at Level 2 as explained here. So Level 3 TCGA data should be post-normalization and in a format more suitable for making interpretations. But different tumor-specific working groups may do the job differently. GBM was one of the earliest TCGA projects where a lot of lessons were yet to be learned - like abandoning U133A for RNA-seq based expression data. ;)
In general, you should read the method's sections in the tumor-specific marker papers. For TCGA GBM, the supplement here explains the "Creation of a unified Expression Dataset", but it's not clear whether this needed to be done on top of the Level 3 data.