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Figure 2 | BMC Bioinformatics

Figure 2

From: Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

Figure 2

Optimized between-group classification applied to sarcoidosis data. In panel A, 24 individuals (solid circles) in the training set (H: healthy controls, SI: sarcoidosis stage I, SII: sarcoidosis stage II/III) and 8 individuals (empty circles) in the test set (283, 286, 287, 289 and 290 as H; 282, 284 and 285 as SII) are classified by a standard BGA using the whole set of genes. Panel B shows the different parameters of OBC as a function of the number of genes used in the analysis: the percentage of between group inertia (solid line), the percentage of good cross-validation (dashed line) and the variance of between group inertia (dot-dashed line). For indication, the percentage of test samples correctly predicted is represented by a dotted line. This parameter was not used in optimization of the training model. The vertical line shows the optimal number of genes. In panel C, the 105 most discriminating genes (initial subset) are located at the periphery of the biplot (black crosses) and the 58 optimal genes are highlighted (circled crosses). In panel D, 8 test-samples are classified using a BGA based on the 58 optimal genes.

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