Noi/NOTES/2012-6-13
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Regression analysis of UCLA SZ data (additional different age cutoff)
- Suggestions from lab meeting on 2012.05.16
- LDA: random choose samples for training and (have UCLA-SZ and UCSD-GA on training and testing data sets)
- LDA: Change age cutoff from 40 to different number (50, 60 or 70) and see the accuracy of classification.
- PCA: I also performed PCA and changed the color of each sample in scatter plot based on the age cutoff.
- Training and testing data set
- list 1-96 =>UCSD-SZ, 97-169 => UCSD-GA
- trainAge <- c(1:40, 91:132)
- testAge <- c(41:90, 133:169)
Tables of raw data
Age cutoff 40 (10% FDR) | Predicted\Truth | Adult | Young adult | Correct | FALSE | Total |
Training | Adult | 54 | 2 | 77 | 5 | 82 |
Young adult | 3 | 23 | ||||
Testing | Adult | 59 | 1 | 85 | 2 | 87 |
Young adult | 1 | 26 | ||||
Cross validation | Adult | 112 | 3 | 161 | 8 | 169 |
Young adult | 5 | 49 |
Age cutoff 50 (10% FDR) | Predicted\Truth | Adult | Young adult | Correct | FALSE | Total |
Training | Adult | 51 | 4 | 76 | 6 | 82 |
Young adult | 2 | 25 | ||||
Testing | Adult | 58 | 0 | 85 | 2 | 87 |
Young adult | 2 | 27 | ||||
Cross validation | Adult | 110 | 4 | 162 | 7 | 169 |
Young adult | 3 | 52 |
Age cutoff 60 (10% FDR) | Predicted\Truth | Adult | Young adult | Correct | FALSE | Total |
Training | Adult | 32 | 7 | 72 | 10 | 82 |
Young adult | 3 | 40 | ||||
Testing | Adult | 40 | 13 | 71 | 16 | 87 |
Young adult | 3 | 31 | ||||
Cross validation | Adult | 72 | 22 | 141 | 28 | 169 |
Age cutoff 70 (10% FDR) | Predicted\Truth | Adult | Young adult | Correct | FALSE | Total |
Training | Adult | 14 | 4 | 70 | 12 | 82 |
Young adult | 8 | 56 | ||||
Testing | Adult | 16 | 8 | 68 | 19 | 87 |
Young adult | 11 | 52 | ||||
Cross validation | Adult | 30 | 12 | 138 | 31 | 169 |
Young adult | 19 | 108 |
Table of accuracy and misclassification rate
Age cutoff | Training (Accuracy of allocation) | Misclassicication rate | Testing (quality of model) | Misclassicication rate | Cross validation | Misclassicication rate |
40 | 77 of 82 | 6.10% | 85 of 87 | 2.30% | 161 of 169 | 4.73% |
50 | 76 of 82 | 7.32% | 85 of 87 | 2.30% | 162 of 169 | 4.14% |
60 | 72 of 82 | 12.20% | 71 of 87 | 18.39% | 141 of 169 | 16.57% |
70 | 70 of 82 | 14.63% | 68 of 87 | 21.84% | 138 of 169 | 18.34% |
PCA plots
File:UCLA-GA age-cutoff40 10FDR pcaplot1.png File:UCLA-GA age-cutoff40 10FDR pcaplot2.png