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Correlation between BCR batch and the processing batch for 27k arrays (January 20, 2012):
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{csv}Batch on the download page,"# after ""HumanMethylation27k"" in the file name, Level 1",Batch as the sixth field in the patient barcode
Batch 1,2,0186
Batch 2,3,0199
Batch 3,4,0218
Batch 4,no data,
Batch 5,no data,
Batch 6,no data,
Batch 7,no data,
Batch 8,no data,
Batch 10,1,0392
Batch 16,5,0521
Batch 20,6,0595
Batch 26,7,0788
Batch 38,8,0915
Batch 62,9,1228
Batch 79,no data,
Batch 111,no data,
Batch 130,no data,
Batch 174,no data,{csv} |
Batch vs clinical traits
Number of clinical traits: 31
Number of batches based on DNA methylation data: 19
Relationship between batch and the center:
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| collapse | true |
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Batch vs clinical traits
Number of clinical traits: 31
Number of batches based on DNA methylation data: 19
Relationship between batch and the center:
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> table(batchID,two) two batchID 02 06 08 12 14 15 16 19 26 27 28 32 41 74 76 81 87 0186 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0199 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0218 0 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0199 17 00242 0 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0218 00279 2834 17 015 0 0 0 0 0 0 0 0 0 0 0 0 0 0 02420287 26 016 5315 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0297 13 02790 3419 17 150 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0314 02872 267 16 156 05 0 0 0 0 0 0 0 0 0 0 0 0 0 0297 130337 0 1910 0 16 0 01 0 0 0 0 0 0 0 0 0 0 0 03140392 20 7 60 10 5 06 0 05 0 0 0 0 0 0 0 0 0 0 03370521 0 10 4 0 1612 12 0 3 1 7 0 6 0 3 0 0 0 0 0 0 0 0 0 03920595 0 74 0 10 4 613 0 51 010 01 04 09 0 0 0 0 0 0 05210788 05 412 0 12 120 3 70 60 30 0 13 010 04 0 0 0 0 0 05950915 0 40 0 9 4 132 0 10 10 9 1 0 4 0 9 0 05 04 0 0 0 0 0788 51228 12 0 01 30 0 02 0 01 13 103 41 0 0 15 4 0 0 0 0 0915 01481 0 05 90 23 0 0 90 0 06 0 11 5 1 40 0 09 0 0 12281697 0 113 0 0 21 01 10 10 3 1 0 03 15 2 4 01 0 05 01 1 1481 0 51844 0 310 0 0 05 0 6 0 11 1 02 0 91 0 01 6 10 16971 0 13 02004 0 17 1 0 10 1 0 3 2 10 0 54 10 10 0 18440 0 10 0 0 5 0 0 1 2 0 1 0 1 6 10 1 0 2004 0 7 0 0 3 0 0 4 0 0 0 0 0 0 0 0 0 |
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Relationship between batch and clinical variable, significant correlations (entire table can be found here)
Survival vs batch
Code for automatic analysis of survival and correlation with clinical traits can be found here.
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