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. 2015 Jan 1;19(1):41–51. doi: 10.1089/omi.2014.0077

Table 2.

Summary of Resampling Results in Training Dataset Using PCA Classification

  Ct standardized
  MGMT-LDHA MGMT LDHA
Estimate Training Test All Training Test All Training Test All
Sensitivity 99.9 91.4 97.5 85.8 85.5 85.7 42.8 42.9 42.9
Specificity 87.3 86.0 86.9 77.7 78.0 77.8 44.4 44.5 44.4
Accuracy 91.0 87.4 89.8 80.1 79.9 80.0 44.0 44.1 44.0
% IDH1 mut GPG 28.6 13.9 21.8 33.2 9.9 20.0 66.6 5.1 15.4
% IDH1 mut PPG 0.0 0.02 0.006 0.0 0.0 0.0 0.0 0.0 0.0
Fold-change PPG/GPG MGMT 11.0 6.2 7.8 19.3 7.2 10.6 23.3 0.6 1.6
% GPG<mean MGMT 85.7 78.9 82.5 100 100 100 100 53.8 61.5
% PPG<mean MGMT 22.1 20.6 21.6 7.2 5.8 6.7 0.0 46.1 25.0
  Ct quantiles normalized+standardized
  MGMT-LDHA MGMT LDHA
Estimate Training Test All Training Test All Training Test All
Sensitivity 100.0 99.9 99.9 100.0 100.0 100.0 39.7 40.4 40.0
Specificity 85.2 81.1 83.8 80.0 80.1 80.0 50.0 50.1 50.0
Accuracy 88.0 85.3 87.0 83.7 84.5 84.0 48.1 48.0 48.0
% IDH1 mut GPG 40.0 15.2 24.4 40.1 13.3 22.2 90.0 5.5 16.7
% IDH1 mut PPG 0.0 0.01 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Fold-change PPG/GPG MGMT 16.4 7.8 9.6 18.8 9.4 11.2 24.5 0.6 1.7
% GPG<mean MGMT 100.0 85.0 90.2 100.0 100.0 100.0 90.0 56.2 66.7
% PPG<mean MGMT 21.8 21.3 21.6 12.5 12.6 12.5 0.0 47.6 23.1

This table depicts the average classification and molecular features across 10,000 iterations. Only those samples having survival data were considered (n=25). Two thirds of cases were used as training set (n=16), and the remaining ones were used as a test set (n=9). The information in this table is equivalent to that provided in Table 1, but in this case the LDA equations were fitted only using the standardized RT-PCR expression values from MGMT and LDHA genes. On the top panel, values were only standardized, while on the bottom one, the Ct values were first normalized by the quantiles method and the same standardization as the one described above was undertaken afterwards.