A bootstrap based methodology is introduced for analyzing repeated measures/longitudinal microarray gene expression data over ordered categories. The proposed non-parametric procedure uses order-restricted inference to compare gene expressions among ordered experimental conditions. The null distribution for determining significance is derived by suitably bootstrapping the residuals. The procedure addresses two potential sources of correlation in the data, namely, (a) correlations among genes within a chip ("intra-chip" correlation), and (b) correlation within subject due to repeated/longitudinal measurements ("temporal" correlation). To make the procedure computationally efficient, the adaptive bootstrap methodology of Guo and Peddada (2008) is implemented such that the resulting procedure controls the false discovery rate (FDR) at the desired nominal level.