Table 1.

Effects of Probe Filters

	Platform Type
Filter	GeneFocus	HG_U95av2	133A	133plus2
Unidentifiable Target	2.19% (0.06%)	2.79% (1.40%)	2.17% (0.02%)	10.80% (0.0%)
SNP	5.92% (12.11%)	1.78% (3.61%)	4.14% (8.47%)	1.94% (4.36%)
Cross-hybridization	60.06% (18.39%)	60.30% (19.47%)	60.30% (18.86%)	62.15% (15.13%)
Biophysical	5.71% (3.60%)	5.16% (3.84%)	5.58% (3.46%)	13.37% (2.81%)

Percent Probes Lost as Total and (Perfect Match).

Number of probes determined to be unusable for each filtering step across several generations of the Affymetrix human gene expression array. The total number of probes in each array is the denominator, values in parentheses refer to the prefect match probes only. Each set was run independently so one does not see the subset of probes that fall into multiple categories, and the totals see to add up to more than the number of probes present. For example, eliminating probes that lack sequence information causes the Biophysical Filter to remove2.47% (2.44% PM) of the probes from the U95Av2 list, rather than 5.17%. Note the Unidentifiable target total for U95Av2 is now 0.06%, some probes have had their status revised since this analysis was first done.