Does the GDC correct for batch effects across samples?

The GDC does not perform batch effect corrections across samples for the following reasons:

• The GDC accepts new data on an ongoing basis and has continuous data processing and frequent release plans. It is operationally difficult to perform cross-GDC batch effect corrections in every release.
• Many of the batch effect correction processes require manual considerations and project-specific knowledge.
• Automatic batch effect correction might remove real biological meaningful signals, especially when batch effect is confounded with real biological effects.

As such, the GDC prefers that users to perform their own batch effect removal.