Page Comparison

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)

{code

}> 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

{code}
Significant correlations of batch with the clinical variables:
{csv}"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
{csv}
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