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

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M1">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M2">View MathML</a>


"Lenient" Rule A: Number of False Positives

RFP × N

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M3">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M4">View MathML</a>


"Stringent" Rule B: Number of False Negatives

RFN × H

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M5">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M6">View MathML</a>


"Stringent" Rule B: Number of False Positives

RFP × N

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M7">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M8">View MathML</a>


"Balanced" Rule C: Number of False Negatives

RFN × H

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M9','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M9">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M10','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M10">View MathML</a>


"Balanced" Rule C: Number of False Positives

RFP × N

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M11','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M11">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/50/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/50/mathml/M12">View MathML</a>


N = The number of genes in the screening library, H = The number of genes a screen should uncover under ideal conditions, RFN = Fraction of reagents of H that fail. RFP = 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".

Booker et al. BMC Genomics 2011 12:50   doi:10.1186/1471-2164-12-50

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