Microarray experiments allow one to examine global patterns of gene expression, but by their nature involve multiple comparisons that can generate false positives. While the idea of removing probe sets that are unlikely to produce positive results is not new, we present a systematic analysis of the effects of several strategies. Not all genes are expressed in any one tissue [3]. Probe sets that have very low signals or are called Absent primarily reflect noise in the data, and give a large number of false positives without adding many true positives. Permutations expected to produce no significant changes confirmed that Absent probe sets have an increased risk of producing false positives (Tables 3 and 6). Requiring that only one treatment group meet the threshold, particularly with our recommended filtering by Fraction Present, preserves data for genes that are turned on or off, genes that may be of great interest to biologists.
