Simulated data set influenced by a single probe-specific biological, two probe-specific adjustment variables, and intensity-dependent
array effects. Data were simulated for a total of 25,000 probes and 50 arrays. The biological variable is a dichotomous variable specifying two groups (Group 1 and Group 2),
with 25 arrays sampled from each group. The dichtomous probe-specific adjustment variables has 5 different levels and mimics a batch effect. The 5 batches each contain
10 samples, and are balanced with respect to the biological grouping factor. The continuous probe-specific adjustment variable is
sampled from a Normal(1,0.1) and mimics an age effect. The baseline probe intensities were sampled from a chi(1,2) distribution.
Any baseline intensities greater than 15 were set to a random value from the
interval [15,16]. The random variation terms were sampled from a Normal(0,0.25) and the array functions were defined by randomly sampling coefficients
for a two-dimensional B-spline basis functions from a Normal(0,1).Randomly selected subsets of 30%, 10%, and 20% of the probes were defined as influenced by the biological groups, batch, and
age variables, respectfully. The magnitude of the biological effects were sampled from a Normal(1,0.3) distribution, the
probe-specific batch effects from a Normal(0,0.3) and the probe-specific age effects from a Normal(1,0.1). An instance of
this simulated data can be generated using the code in the examples section below.