Hello,
Is it possible to get a description on how GLASS handled the TCGA samples included in GLASS data, which TCGA data level is downloaded and how you processed it? I am particularly interested in this Glass Gene expression data downloaded from Synapse: https://www.synapse.org/Synapse:syn57367276
Best,
Mariyam.
Created by Mariyam Khan mariyam_khan Hi Mariyam,
The TCGA samples that were part of the GLASS gene expression matrix were processed as described in the Methods section of the associated manuscript. Specifically, RNAseq fastq files from the Low Grade Glioma (LGG) and Glioblastoma Multiforme (GBM) projects in TCGA were obtained from the Genomic Data Commons legacy archive (https://portal.gdc.cancer.gov/legacy-archive/) and then processed as described in the RNA preprocessing subsection of the Methods. I hope this helps!