If a group of arrays have been analyzed and there are new arrays coming in, one can combine the old and new arrays together as a new group and redo normalization (if needed check “Ignore the normalized data” to make sure all arrays are normalized to the same baseline array) and the model-based expression. If it is not desired to have the expression values of the old arrays changed, one can use the probe sensitivity index file of the old group to analyze the new arrays.
For the above old and new groups of arrays, or when the two groups of array are analyzed separately, the resultant expression indexes are generally not comparable for the same probe set. This is because the arrays in each group may be normalized to different baseline array (thus having different overall signal brightness), and the model-based expression indexes for the same probe set may be based on different subsets of probe pairs in the two groups. The latter is due to probe outlier detection; usually the probe sensitivities vary, and inclusion or exclusion of a probe may yield large differences in expression values. However, the relative expression between samples in terms of fold change should remain similar. For example, one scheme estimates the expression values as 100 and 200 for two samples, and another scheme gives 500 and 1000; the two are equivalent since expression values for one probe set are relative measure of the underlying mRNA concentrations.