Important update (January 20th, 2011): the data below have been corrected for the BCR batch which is not necessarily the processing batch. The dataset needs to be reanalyzed.

Correlation between BCR batch and the processing batch for 27k arrays (January 20, 2012):

Correlation of batch with clinical traits

Date: December 20th, 2011

Number of batches based on DNA methylation samples (not necessarily available samples): 10

Correlation of batch with clinical traits (complete table) can be found here

Cross-tabulation of batch vs center (two=second field in the patient barcode)

> table(batchID,two)
       two
batchID 05 35 38 44 49 50 53 55 64 67 71 73 75 78 80 86 91 93 95 97 99
   0945  0  1  0  7  0  0  0  4  4  5  0  0  0  0  0  0  0  0  0  0  0
   1104  3  2  0  7  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
   1205 14  0  6  1  7  0  0  0  0  0  0  7  0  0  0  0  0  0  0  0  0
   1551  0  0  3 10  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
   1626  6  1  0  2  0  7  0  1  6  0  0  0  2  0  1  0  0  0  0  0  0
   1756  3  0  3  5  1 13  0  1  0  4  0  2  9  0  0  1  0  0  0  0  0
   1856  8  0  0  6  9  6  0  2  0  0  1  0  0  0  0  0  5  0  0  0  0
   1947  0  0  0  0  1  1  0 16  0  0  0  0  5  0  2  1  5  0  2  0  0
   2037  0  0  1  1  0  1  0  6  0  0  0  0  0 17  0  0  0  1  0  5  1
   2064  0  0  0  9  0  0  2  1  2  0  0  0  0 11  0  2  0  0  1  0  0

Significant correlations of batch with the clinical variables:

Most likely that days to form completion is not a real clinical trait.
DNA methylation data (tumor matched): 27k, available 32 patients. At this point it is not enough to proceed with analyses