Figure 2.

Experimental design for the microarray studies. The indicated time periods of 1, 2, and 3 represent weeks post-lentectomy from time 0 (Control). Each mouse represents a biological replica for a given experimental condition. An arrow denotes a microarray slide comparison between a given pair of mice. Arrows for a given experimental comparison represent "dye flips". Our statistical model does indeed unequivocally factor out the gene-specific dye effect from the estimates of differential expression. This is achieved by fitting a linear statistical model with a "dye" effect, as described in the data normalization and analysis section of the methods, to each gene separately. This approach has been demonstrated to work well in unbalanced situations such as the week 2 and 3 comparisons [35].