Experiment: The experiment uses a common reference design; 23 samples are hybridized with the reference sample RNA. The 23 samples are from 6 treatment groups: xDS, xDL, xMS, xML, xMRS, and xMRL, respectively. About 1000 “marker” genes are chosen based on the p-values for each gene using one-way anova (or t-test). PCA is performed on the (relative) expression levels of genes in each sample. The three axes in the figure are the first three principal components calculated by linearly transforming the original gene expression levels. As shown in the figure, some samples belonging to the same groups are well separated from others.
