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.
