Effects of filtering by Present call on analysis of microarray experiments

BMC Bioinformatics

Table 4 Number of on/off probe sets retained after filtering at selected thresholds.

IFN data	Unfiltered	FP>0 sig 254	FP25 sig375	FP50 sig475	FP75 sig593	FP100 sig795
Fraction Present	108	108	108	108	90	34
Average Signal	108	104	100	89	81	64
Vitamin A data		FP>0 sig 200	FP25 sig265	FP50 sig323	FP75 sig400	FP100 sig475
Fraction Present	31	31	31	31	27	16
Average Signal	31	26	22	17	16	13

Filtering by Fraction Present (FP) and average MAS5 signal (sig) followed by threshold. On/off: probe sets with p < 0.05 for t-test and in which the sum of Present calls differed by more than 6 for IFN data and more than 4 for vitamin A data between the two treatment groups were called turned "on" or "off".

ISSN: 1471-2105