Table 3.

Model of RNAi reagent disambiguation methods under one, two or three reagents per gene.

	1 RNAi Reagent/Gene	2 RNAi Reagents/Gene	3 RNAi Reagents/Gene
"Lenient" Rule A: Number of False Negatives	RFN × H	$R_{FN}^2\times H$	$R_{FN}^3\times H$
"Lenient" Rule A: Number of False Positives	RFP × N	$\left(R_{FP}^{}\times 2-R_{FP}^2\right)\times N$	$\left(R_{FP}^{}\times 3-R_{FP}^2\times 3+R_{FP}^3\right)\times N$
"Stringent" Rule B: Number of False Negatives	RFN × H	$\left(R_{FN}\times 2-R_{FN}^2\right)\times H$	$\left(R_{FN}\times 3-R_{FN}^2\times 3+R_{FN}^3\right)\times H$
"Stringent" Rule B: Number of False Positives	RFP × N	$R_{FP}^2\times N$	$R_{FP}^3\times N$
"Balanced" Rule C: Number of False Negatives	RFN × H	$\left(R_{FN}\times 2-R_{FN}^2\right)\times H$	$\left(R_{FN}^2\times 3-R_{FN}^3\times 2\right)\times H$
"Balanced" Rule C: Number of False Positives	RFP × N	$R_{FP}^2\times N$	$\left(R_{FP}^2\times 3-R_{FP}^3\times 2\right)\times N$

N = The number of genes in the screening library, H = The number of genes a screen should uncover under ideal conditions, R_FN = Fraction of reagents of H that fail. R_FP = Fraction of reagents of N that are false positives. Rule "A": Only one reagent targeting a gene need to be a "hit" for the gene to be called a "hit". Rule "B": All reagents targeting a gene need to be a "hit". Rule "C": More than half of reagents must score as a "hit".