Note that many of these files are large and take some time to download. Depending on connection speed, you may see an alert from your browser about a slow running script; please allow the script to continue running for an amount of time commensurate to the number of files selected.
Before using TCGA data, please read TCGA guidelines for publication and moratoriums.
Before using TCGA data, please read TCGA guidelines for publication and moratoriums.
When analyzing the RPPA data:-
For a single disease profiled in a single RPPA batch, either Level 3 (L3) or Level 4 (L4) should be good for single-disease analysis.
-
For a single disease profiled in multiple batches, L4 is definitely better than L3 for single-disease analysis because of batch effects among different batches.
-
For multiple disease analysis, the merged Pan-Can 19 L4 data should be used. The pan-cancer analysis beyond the Pan-Can 19 is an ongoing effort; and users are encouraged to join the TCGA Pancan working group if they are really interested in.