Repeated Measurements on Distinct Scales With Censoring—A Bayesian Approach Applied to Microarray Analysis of Maize

Abstract

We analyze data collected in a somatic embryogenesis experiment carried out on Zea mays at Iowa State University. The main objective of the study was to identify the set of genes in maize that actively participate in embryo development. Embryo tissue was sampled and analyzed at various time periods and under different mediums and light conditions. As is the case in many microarray experiments, the operator scanned each slide multiple times to find the slide-specific ‘optimal’ laser and sensor settings. The multiple readings of each slide are repeated measurements on different scales with differing censoring; they cannot be considered to be replicate measurements in the traditional sense. Yet it has been shown that the choice of reading can have an impact on genetic inference. We propose a hierarchical modeling approach to estimating gene expression that combines all available readings on each spot and accounts for censoring in the observed values. We assess the statistical properties of the proposed expression estimates using a simulation experiment. As expected, combining all available scans using an approach with good statistical properties results in expression estimates with noticeably lower bias and root mean squared error relative to other approaches that have been proposed in the literature. Inferences drawn from the somatic embryogenesis experiment, which motivated this work changed drastically when data were analyzed using the standard approaches or using the methodology we propose.

Expression Profile of Maize (Zea mays L.) Embryonic Axes During Germination: Translational Regulation of Ribosomal Protein mRNAs

“…Microarray technology for maize (Zea mays L.) studies has recently been applied to evaluate gene expression of different tissues and developmental stages (Lee et al 2002, Liu et al 2008, Zhu et al, 2009, such as in juvenile vs. adult leaves from culture-rejuvenated plants (Strable et al 2008) and in somatic embryogenesis during embryonic development (Love and Carriquiry 2009). However, at present, there is no report supported by microarray technology for maize seed germination, a critical developmental plant process.…”