GeneData

This project introduces some basics about downloading gene expression datasets from GDC and firebrowse repositories. This project uses R for downloading and pre-processing the data.

To download Data from FireBrowse

• http://gdac.broadinstitute.org/
• Select "Breast invasive carcinoma" -> "data" -> "Browse".
• From "mRNASeq" select "illuminahiseq_rnaseqv2-RSEM_genes_normalized" and save it on your computer.
• Unzip the folder and rename it to RNA.

To Download and process data from GDC/TCGA

• TCGA repository https://portal.gdc.cancer.gov/
• use Download_Analyze_TCGA.R to download and analyse the data -The code normalize the data to extract 19k+ genes from the originally 20k+, then only the def. expresessed genes (3k+) were selected.
• we scaled [0 mean and one unit variance] the def. expressed genes across genes.
• the code generates 3 different files: (1) scaled Normal samples: samplesNT_scaled.csv (2) scaled tumor samples: samplesTP_scaled.csv (3) a scaled data file combining both normal and tumor samples: All_samples_scaled.csv