Gene Expression Analysis of Exposure

The inverted TIFF images were processed with Mapix (Innopsys) to ascribe a value to the spot intensity, which was corrected for background intensity. The intensity data were normalized within and between arrays using the Bioconductor package limma using the control reference genes RPL8 and actin. To test for differential expression, the bayesian adjusted t-statistics from the linear models for Microarray data (limma) package was used on the combined dataset [28 (link), 29 ]. The combined dataset possesses the data originating from 8 biological replicates and the technical repetition was also included. Adjusted p-values were calculated using the method developed by Benjamin and Hochberg [30 ]. The differential expression was calculated by comparing the expression data from an exposed experiment with its corresponding control experiment. Thus, the exposed cage experiments were compared with the non exposed cage experiments from the same exposure time and the exposed field experiments were compared to the non-exposed field experiments with the corresponding exposure time.