Frequently Asked Land Questions
From Array Suite Wiki
1. Where can I find the TCGA marker paper?
You can find the TCGA maker paper here
2. What are the meanings of different terms in TCGA metadata and clinical data?
TCGA provides a brief "dictionary" for its terminology. Users can find it here
3. I noticed that you have very updated and rich metadata for TCGA patient population.I was particularly interested in subtype annotation you have for various cancer-types such as Colon CRC [Expression][Cluster], Glioblastoma GBM [Expression][Cluster], Breast BRCA [PAM50], etc. Can you please provide source information (publication etc.) that you used to annotate samples across all disease-type?
Clusters and cancer subtype classifications are extracted from TCGA marker papers (https://tcga-data.nci.nih.gov/docs/publications/).
4. Have you validated the signature or just used what was in the publications?
Currently, we only provide signatures and clusters listed in the publications
5. How can I find the pipeline for different data types in TCGA Land?
Omicsoft re-process the RNAseq data while other data types' pipeline can be found here:
6. What is controlled access data and how can I get access?
The Controlled Access data tier contains data that may be unique to an individual. These data require user certification for access. To get more information from Omicsoft on how to apply for access please provide the requested information here http://www.omicsoft.com/data-coapplications: