What does "Level 3" mean in "Level 3 TCGA tumor samples"? Are there Level 2 and Level 1 also. Please explain.

The Genomic Data Commons (GDC) has actually done a very good job with their documentation, and information pertaining to the levels of access to the TCGA (and other) data is there to be found via a search. Please take a look at just these two pages:

• Data Levels
• The GDC for TCGA Data Access Matrix Users

Essentially 'Level 3' data is open access - anybody can use it, from your teacher to the local greengrocer to the leader of your country, and you can use it, too. Level 3 data has already passed through an amount of processing, which means that you are restricted by whatever analytical methods have already been used. Level 3 mutation data, as an example, typically comprises somatic variants in Mutation Annotation Format (MAF), which is a tab-delimited format specification devised during the TCGA project.

Level 1 and 2 data are controlled. You will required authorisation via dbGaP in order to access these. Using Level 1 data, however, provides for most flexibility in your analysis methods, but not everybody can deal with this data for different reasons, such as IT infrastructure, expertise, etc.

Kevin