R Program for Serial Dilution Curve

for analysis of reverse phase protein array data

The R program was written to analyze reverse phase protein array (RPPA) data.

· To download the R program, please click here.

· For help to use the R program, click here.

· The manuscript that describes the method can be found here.

· To cite the method, use:

Zhang L, Wei Q, Liu W, Mills GB, Coombes KR. Serial dilution curve: a new method for analysis for reverse protein array data. Submitted to Bioinformatics. 2008.

Serial dilution plot. Each point in the serial dilution plot is composed of an observed signal S_k at dilution step k (on x-axis) and a corresponding signal S_k+1 of the same sample at the dilution step k+1 (on y-axis). The curve was produced using the following equation:

S_k = a + d^γ (S_k+1 – a) / [1+ (d^γ –1) (S_k+1 – a) / (M - a)]

The curve has two intersection points with the identity line: (a,a) and (M,M). a is background level; M is the saturation level; d is the dilution step. γ is a factor in Sip’s model.

Abstract of the manuscript:

Reverse phase protein arrays (RPPA) are a powerful high throughput tool for measuring protein concentrations in a large number of samples. In RPPA technology, the original samples are often diluted successively multiple times, forming dilution series to extend the dynamic range of the measurements and to increase confidence in quantitation. An RPPA experiment is equivalent to running multiple ELISA assays concurrently except that there usually is no known protein concentration from which one can construct a standard response curve. Here we describe a new method called “serial dilution curve for RPPA data analysis”. Compared with the existing methods, the new method has the advantage of using fewer parameters and offering a simple way of visualizing the raw data. We showed how the method can be used to examine data quality and to obtain robust quantification of protein concentrations.