This archive contains the Level 3 data of 127 BLCA samples for the TCGA project.

All the 54 samples assayed in version 1.0.0 are included here. Therefore we encourage
users to use this revision of the data.

The data are in log2 scale. 

Level 3 data are derived from Level 2 data. 
The normalization is described
as follows:

1) Starting with a level 2 data matrix, 
median center the data of each protein;
2) From 1), calculate the median value for each sample;

3) subtract the sample medians from 2) from the level 2 data of the corresponding samples.


This method has proved to work well. 
However, the savvy user is encouraged try other 
normalization methods if she likes.



A word about batch effect correction: 

There may be two or more 
batches for certain cancer types, e.g. BRCA, UCEC, OV, etc.
We are working on methods of 
batch effect alleviation that is 
specific to this platform. 
currently, if there is more than one batch,
the batches are normalized separately and uploaded as is. 









-MDACC