PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.

ABSTRACT: The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts fo

SUBMITTER: Qiao W 

PROVIDER: S-EPMC3527275 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature