at low signal values. Removing probe sets in which fewer than half of the arrays in at least one of the experimental groups was called Present eliminates the large shoulder of Absent probe sets, leaving a distribution that is more nearly normal (Fig. 1B). It is important to note that the signals for all samples in a particular probe set are treated as a group; all are retained or all removed based on whether at least one experimental group (interferon treated or control, in this example) meets the filtering criterion. In Fig. 1, signal values for probe sets for individual samples are shown, hence the retention of some Absent samples after filtering. An alternative method of removing probe sets thought to represent genes with little or no expression is to set a minimum average signal level for at least one of the two experimental groups. Fig. 1C shows the distribution of signal values when a minimum average signal of 475 is required; 475 was chosen to retain a similar number of probe sets as the 50% Present filter shown in Fig. 1B. Filtering based on the signal values more severely truncated the low expression values (Fig. 1C).
