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. 2009 Sep 18;5(9):e1000512. doi: 10.1371/journal.pcbi.1000512

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Ji et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) SDRS analysis of intensity data for probeset 205016_at (Transforming Growth Factor Alpha), following a four hour treatment with dasatinib. The plot shows the maximal F-statistic obtained for this probeset at each C value evaluated by SDRS. The critical value of the F-distribution at P<0.05 is indicated. The global maximal F was obtained from fit of experimental data to a sigmoidal dose response model with the values of A, B, C, D shown. (B) The experimental data for probeset 205016_at, and the curve obtained using the optimal model parameters established by SDRS in the equation shown. (C) Schematic diagram of the data analysis flow. The SDRS report (left) contains the calculated pharmacological parameters for each probeset, and can be used to identify individual response transcript of interest. This report is qualitatively similar to the output of an iterative algorithm. The SDRS Summary Doses output (right) is unique to the grid search method. This dataset is used for the further approaches shown, which characterize and compare the overall transcriptional responses. A more detailed flowchart of SDRS is provided in Text S1.