mdanderson.org_BRCA_MDA_RPPA_Core

Created By Kyle Ellrott kellrott
This archive contains the Level 3 data of 410 TCGA BRCA samples and 47 control samples (7 unique cell lines or pool of cell lines), generated by the RPPA Core Facility at the University of Texas M. D. Anderson Cancer Center. The data are normalized protein expression values in log2 scale. The normalization starts with median centering the data of each antibody or slide, then calculate a median value for each of the samples, and subtract the sample medians from the orignal data. For cell line samples, this normalization step may not be critical, but for tumor tissue samples, it is critical because the total proteins onto the slide can vary tremendously for different samples. If one would like to try a different normalization method, he or she can start with the level 2 data. Similar to the Level 2 data and different from the Level 1 data, each file here corresponds to a single sample. As in the Level 2 data, the two columns are Antibody.Name and Protein.Expression. The antibody names in the files (Levels 1, 2 and 3) can be matched to standard HUGO gene symbols in the antibody annotation file "mdanderson.org_BRCA.antibody_annotation.txt" in the mage-tab archive.

freeze: tcga_pancancer_v4
acronym: BRCA
disease: cancer
species: Homo sapiens
fileType: genomicMatrix
platform: MDA_RPPA_Core
dataCenter: mdanderson.org
dataSubType: RPPA