Figure 8

Normalised log₂ intensities for all non-spikes on strip 1 of a particular array in the experiment grouped according to the number of As, Ts, Gs or Cs in the probe sequence. The normalised log₂ intensities and bead type variances are also shown in terms of GC content. The width of each box is proportional to the number of observations. Probes with higher GC content are shown to have higher intensity on average and a lower variance. Finally, estimated effect sizes are shown for each base position relative to having a T at that position. The normalised intensities are seen to be higher if a G or C is present at the first base in the sequence and have a lower variance. However, no other systematic trend is seen.