Examination of tag levels and fold-change in each of the SAGE library comparisons considered in Figure 4. The data is plotted in a log scale in rotated coordinates, where log2(xy) serves to indicate tag levels in the two libraries (where x = tag levels in SAGE library A, and y = tag levels in SAGE library B) and log2(y/x) serves to indicate fold changes in tag levels. Tags with a count of zero in either library were omitted from the analysis. The dark lines indicate the two standard deviation confidence limit calculated for the distribution of tags in Figure 5c (that is, same starting mRNA, different SAGE libraries) using a locally weighted smoothing technique based on the standard deviations in the neighborhood of each point. This is done to allow ready comparison of the observed tag differences between SAGE libraries to the baseline level of variability expected from SAGE library construction. (a) Sampling, ONL1 vs ONL2 (same library, different tags); (b) ditag, P2.5A vs P2.5B (same ditag ligation, different libraries); (c) mRNA, crx+/+A vs crx+/+B (same starting mRNA, different libraries). (d) 44-year-old vs 41-year-old, libraries from peripheral retina from different similar-aged males; (e) 88-year-old vs 44-year-old, libraries from peripheral retina from individuals that differ in age and sex; (f) littermates, P6.5A vs P6.5B (libraries made from retinas of three P6.5 C57B/6 mice vs libraries made from retinas of three littermates); (g) environment, hypothalamus A vs hypothalamus B (libraries made from hypothalami of 3 8-week-old male C57B/6 mice housed in Boston, MA vs libraries made from hypothalami of 20 8-week-old male C57B/6 mice housed in Melbourne, Australia); (h) retina vs hypothalamus, libraries from adult male C57B/6 mouse retina vs adult male C57B/6 mouse hypothalamus; (i) retina vs 3T3 cells, libraries from adult male C57B/6 mouse retina vs mouse 3T3 fibroblast cell line. See Table 1 and Materials and methods for more information about these SAGE libraries.