Is it representative to use the minimal matched data of RNA-Seq in TCGA?

Question

[Zahra]

Hi all,

As far as I understood, the number of "solid tissue normal" data in TCGA is minimal, and given this, I have two questions:

1. For DE analysis that we need the matched data of normal and tumor tissue, is it representative to use these minimal data? Are there any alternatives?
2. What is the significance of tumor tissue RNA-Seq data without their matched normal data?

Thanks for any comment

Answer 1

[Zhenyu Zhang]

1. don't use TCGA normal samples for you purpose. Many of them are perinormals in nature.
2. there are tons of TCGA RNA-Seq based papers published without normals