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Stat Interface. 2012;5(1):89-98.

Generalized Linear and Mixed Models for Label-Free Shotgun Proteomics.

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1
Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, The University of Texas Medical Branch, Galveston, TX 77555.

Abstract

Label-free shotgun proteomics holds great promise, and has already had some great successes in pinpointing which proteins are up or down regulated in certain disease states. However, there are still some pressing issues concerning the statistical analysis of label-free shotgun proteomics, and this field has not enjoyed as much dedication of statistical research towards it as microarray research has. Here we reapply previously used statistical methods, the QSpec and quasi-Poisson, as well as apply the negative binomial distribution to both a control data set and a data set with known differential expression to determine the successes and failure of each of the three methods.

PMID:
22822415
PMCID:
PMC3399744
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