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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 23,1,0689
Batch 31,2,0848
Batch 39,3,0979
Batch 53,4,1096
Batch 60,5,1198
Batch 77,no data,
Batch 101,no data,
Batch 140,no data,
Batch 159,no data,
Batch 181,no data,
Batch 193,no data,{csv} |
Batch vs clinical traits
Number of batches is 12. Correlation between batch and center:
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Batch vs clinical traits
Number of batches is 12. Correlation between batch and center:
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table(two,batchID) batchID two 0689 0848 0979 1096 1198 1440 1551 1633 1818 1871 1947 2043 18 0 0 12 2 0 2 0 2 0 0 0 0 21 13 0 0 0 0 12 20 0 24 0 20 0 0 22 0 9 0 21 0 13 0 0 06 03 0 012 42 0 02 0 33 0 220 90 0 0 04 65 30 0 12 21 0 21 0 3334 0 06 0 0 40 52 0 01 17 01 1 0 3437 0 60 02 06 01 20 0 1 70 10 10 0 3739 0 0 20 60 10 012 0 10 04 0 0 0 3943 0 03 02 0 0 120 02 01 4 0 01 0 4346 0 30 25 0 0 0 20 10 42 0 10 0 4651 0 0 50 03 0 0 0 0 20 0 0 01 5156 01 0 0 30 0 0 0 02 02 0 0 16 60 56 0 120 0 0 01 0 0 0 21 2 0 02 63 6 600 0 200 0 0 12 0 0 01 10 24 0 66 2 0 63 18 015 0 06 0 0 20 0 0 10 0 470 0 66 0 18 0 15 0 60 0 0 0 02 0 0 0 7077 0 0 0 0 0 0 0 0 20 0 04 010 7779 0 0 0 0 0 0 0 0 0 0 1 4 100 7985 0 0 0 0 0 0 0 0 03 0 1 0 8590 0 0 0 0 0 0 0 0 30 0 1 0 9092 0 0 0 0 0 0 0 0 0 0 1 0 92 2 094 0 0 0 0 0 0 0 0 0 0 21 94 0 096 0 0 0 0 0 0 0 0 0 1 0 96 0 02 098 0 0 0 0 0 0 0 0 2 98 0 0 0 0 0 0 0 0 0 0 0 11 |
Significant batch/clinical traits correlations (complete list can be found here):Wiki Markup
Batch vs survival
Again, for this type of cancer clinical traits file contains days to last known alive but it has more NAs than days to the last follow up so I will use the latter for construction of the survival object.
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