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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.