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):
Batch on the download page,"# after ""HumanMethylation27k"" in the file name, Level 1",Batch as the sixth field in the patient barcode,Comments
Batch 34,3,0752,
Batch 37,"1, 2","0945, 1104","0945 comes from 1, one sample that is 1104 comes from 2"
Batch 52,2,1104,
Batch 58,4,1205,
Batch 84,no data,,
Batch 119,no data,,
Batch 144,no data,,
Batch 160,no data,,
Batch 166,no data,,
Batch 183,no data,,
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:
"LUAD_clinical_traits","DataType","NumberOfNAs","Test","Pvalue"
"distant_metastasis_pathologic_spread","factor",115,"Pearson's Chi-squared test",5.22E-09
"days_to_form_completion","integer",124,"Kruskal-Wallis rank sum test",6.42E-04
"year_of_initial_pathologic_diagnosis","integer",108,"Kruskal-Wallis rank sum test",1.98E-03
"vital_status","factor",108,"Pearson's Chi-squared test",4.50E-03
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