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Figure 4 | BMC Genomics

Figure 4

From: SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data

Figure 4

The spider charts 1 to 14 (referring to experiments 1–14) present the number of true positive probe sets that were identified by the SiPaGene optimized filter strategy. The number of the chart indicates the Latin Square experiment that was compared to all other 13 experiments. The comparisons are displayed in the sequence of the Latin Square spiking groups 1 to 14 in clockwise order. For example, in spider chart 1, the Latin Square experiment 1 was compared to all others. The label "1–2" indicates the comparison of experiments 1 with experiment 2. Here close to 50 of the 65 true positive probe sets were identified. The charts "SAM 8" and "dChip 8" present the recall of true positives comparing the Latin Square experiment 8 with all other experiments and applying the software tools SAM and dChip, respectively. The black dot in each chart is located between the comparisons of the Latin Square group as indicated by the chart number with the experiments next to it in the Latin Square table. These are the comparisons with only one titer step of difference in the concentration of the spiked sequences. Therefore, the dot indicates those comparisons that are expected to present with the lowest recall rates. On the other hand, opposite to the dot, the highest recall rates can be expected and were indeed identified with 60 or more true positives.

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