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Calculation of PDS

FF Francesc Font-Clos
SZ Stefano Zapperi
CP Caterina A.M. La Porta
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PDS were first introduced by Drier et al., 201320 as a way of quantifying the overall deregulation of a given pathway, with respect to a reference sample. They are computed by fitting a non-parametric, non-linear one-dimensional curve through the “middle” of the transcriptomic data, in the subspace generated by the genes of that pathway. In practice, this is usually done via the principal curve algorithm,34 although other procedures would be acceptable. We follow the steps carefully explained in ref. 20, except for the following modification: the value of 0 is placed at the mean value of the reference sample, instead of at the extremal point of the curve. This modification can alter the values as computed in ref. 20 only by a linear shift, and makes the results more robust to the variability of the reference sample.

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