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UCEC uterine corpus endometrioid carcinoma

UCEC uterine corpus endometrioid carcinoma

Jan 20, 2012

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. 

Batch vs clinical traits

Number of clinical traits: 57, number of theoretical DNA methylation batches: 20

Correlation of batch with the center

> table(batchID, center) center batchID A5 AJ AP AW AX B5 BG BK BS D1 DF DI E6 EC EO EY FI H5 A00U 0 0 9 0 13 0 0 2 0 0 0 0 0 0 0 0 0 0 A039 18 0 13 0 2 7 6 0 0 0 0 0 0 0 0 0 0 0 A105 7 0 4 0 1 7 13 1 14 0 0 0 0 0 0 0 0 0 A10A 1 0 0 0 1 0 3 0 3 0 0 0 0 0 0 0 0 0 A10N 0 0 0 0 1 7 3 0 1 8 0 0 0 0 0 0 0 0 A10Q 7 0 4 0 1 7 13 1 14 0 0 0 0 0 0 0 0 0 A123 4 0 4 0 4 13 4 3 4 11 0 0 0 0 0 0 0 0 A12K 0 0 0 0 0 0 5 0 1 40 0 1 0 0 0 0 0 0 A138 0 0 12 0 15 0 0 0 0 0 0 3 0 0 0 0 0 0 A13K 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 20 0 0 A145 0 0 0 0 0 4 0 0 0 0 0 0 2 0 0 1 0 0 A14H 3 0 1 0 0 5 0 0 2 6 0 0 1 1 0 2 0 0 A14N 1 0 0 0 0 2 0 0 0 1 0 0 0 0 0 2 0 0 A161 0 2 0 1 0 0 3 0 0 0 0 1 0 0 3 2 0 0 A16G 0 0 0 0 0 0 2 1 0 2 0 1 0 2 0 0 0 0 A17F 0 0 0 0 9 1 1 0 0 4 0 0 0 0 0 0 13 0 A17H 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 A17Z 3 0 0 0 3 0 0 0 0 1 5 0 0 0 5 0 0 1 A18O 2 5 0 0 3 0 1 0 0 0 1 1 0 0 3 2 1 0 A19Z 0 6 0 0 0 4 1 0 0 2 0 2 2 0 7 3 0 0

Correlation with clinical traits (complete table is ) 

 

Batch vs survival

Call: coxph(formula = survivalObject ~ batchVector) n= 369, number of events= 29 coef exp(coef) se(coef) z Pr(>|z|) batchVectorA039 3.652e-01 1.441e+00 8.239e-01 0.443 0.6576 batchVectorA105 -4.042e-01 6.675e-01 1.000e+00 -0.404 0.6862 batchVectorA10A -1.746e+01 2.609e-08 8.054e+03 -0.002 0.9983 batchVectorA10N -1.750e+01 2.510e-08 6.350e+03 -0.003 0.9978 batchVectorA123 -5.327e-02 9.481e-01 9.163e-01 -0.058 0.9536 batchVectorA12K 1.225e+00 3.405e+00 8.810e-01 1.391 0.1643 batchVectorA138 -7.666e-01 4.646e-01 1.225e+00 -0.626 0.5315 batchVectorA13K 1.542e+00 4.675e+00 9.249e-01 1.667 0.0954 . batchVectorA145 -1.745e+01 2.644e-08 1.376e+04 -0.001 0.9990 batchVectorA14H -1.650e-01 8.479e-01 1.240e+00 -0.133 0.8942 batchVectorA14N -1.745e+01 2.639e-08 1.486e+04 -0.001 0.9991 batchVectorA161 2.565e+00 1.301e+01 1.286e+00 1.994 0.0461 * batchVectorA16G -1.744e+01 2.657e-08 1.697e+04 -0.001 0.9992 batchVectorA17F 1.342e+00 3.829e+00 8.677e-01 1.547 0.1218 batchVectorA17Z -1.746e+01 2.602e-08 1.347e+04 -0.001 0.9990 batchVectorA18O 1.955e+00 7.066e+00 1.001e+00 1.953 0.0509 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 batchVectorA039 1.441e+00 6.940e-01 0.28660 7.244 batchVectorA105 6.675e-01 1.498e+00 0.09396 4.742 batchVectorA10A 2.609e-08 3.832e+07 0.00000 Inf batchVectorA10N 2.510e-08 3.985e+07 0.00000 Inf batchVectorA123 9.481e-01 1.055e+00 0.15737 5.712 batchVectorA12K 3.405e+00 2.937e-01 0.60563 19.143 batchVectorA138 4.646e-01 2.153e+00 0.04209 5.127 batchVectorA13K 4.675e+00 2.139e-01 0.76293 28.647 batchVectorA145 2.644e-08 3.783e+07 0.00000 Inf batchVectorA14H 8.479e-01 1.179e+00 0.07459 9.639 batchVectorA14N 2.639e-08 3.790e+07 0.00000 Inf batchVectorA161 1.301e+01 7.689e-02 1.04492 161.869 batchVectorA16G 2.657e-08 3.763e+07 0.00000 Inf batchVectorA17F 3.829e+00 2.612e-01 0.69893 20.972 batchVectorA17Z 2.602e-08 3.844e+07 0.00000 Inf batchVectorA18O 7.066e+00 1.415e-01 0.99266 50.292 Rsquare= 0.064 (max possible= 0.545 ) Likelihood ratio test= 24.27 on 16 df, p=0.08375 Wald test = 18.5 on 16 df, p=0.2953 Score (logrank) test = 30.57 on 16 df, p=0.01524
DNA methylation

27k, M value, didn't split into red and green. Had to remove two arrays that had NA value for unmethylated or methylated probe intensities (TCGA-A5-A0VQ-01A-11D-A10Q-05,TCGA-BS-A0UF-01A-11D-A10Q-05). Ended up with 115 arrays total.