Annotation of gene expression TCGA data

Question

[atemedorri137798]

I have a question about downloaded gene expression TCGA data. I need your guidance please.

According to TCGA documentation : leve1 gene expression and leve2 gene expression data are Controlled-Access. So as I haven't authorisation via dbGaP it should be impossible for me to download them. But after download PAAD TCGA gene expression dataset with TCGAbiolinks , I used SummarizedExperiment package's function ( SummarizedExperiment::rowRanges ) on PAAD downloaded data wich result in gain a data frame with couple of columns and it was strange that one of column's name was "level" and it include 1,2,3 value !!!!!! I expected to get just level 3 gene expression data wich has undergone additional processing steps ,not level1,2 wich are raw gene expression data. I got confused :((

Answer 1

[Zhenyu Zhang]

Talking about level 1/2/3 data is so 10 years ago. You must have read some outdated doc "According to TCGA documentation : leve1 gene expression and leve2 gene expression data are Controlled-Access. "