Physics-based analysis of Affymetrix microarray data

We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained before for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin, rather than being a problem with the proposed model.Comment: 11 pages, 10 figure

The Metaphysics of Paul Weiss

This thesis is an exposition of the metaphysical position set down by Paul Weiss in his Modes of Being. It is written in answer to the question, How is it that there are four irreducible modes of being as held by Paul Weiss? While the bulk of material with which this thesis deals derives directly from Modes of Being, several of Weiss\u27 central arguments in support of his position were taken from an earlier work, Reality, written in 1939. The fundamental metaphysical positions of both works are compatible with one another

Dynamics of the Pionium with the Density Matrix Formalism

The evolution of pionium, the $\pi^+ \pi^-$ hydrogen-like atom, while passing through matter is solved within the density matrix formalism in the first Born approximation. We compare the influence on the pionium break-up probability between the standard probabilistic calculations and the more precise picture of the density matrix formalism accounting for interference effects. We focus our general result in the particular conditions of the DIRAC experiment at CERN.Comment: 14 pages, 2 figures, submitted to J. Phys. B: At. Mol. Phy