poolMC: Smart pooling of mRNA samples in microarray experiments

Background: Typically, pooling of mRNA samples in microarray experiments implies mixing mRNA from several biological-replicate samples before hybridization onto a microarray chip. Here we describe an alternative smart pooling strategy in which different samples, not necessarily biological replicates, are pooled in an information theoretic efficient way. Further, each sample is tested on multiple chips, but always in pools made up of different samples. The end goal is to exploit the compressibility of microarray data to reduce the number of chips used and increase the robustness to noise in measurements. Results: A theoretical framework to perform smart pooling of mRNA samples in microarray experiments was established and the software implementation of the pooling and decoding algorithms was developed in MATLAB. A proof-of-concept smart pooled experiment was performed using validated biological samples on commercially available gene chips. Differential-expression analysis of the smart ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Raghunandan M. Kainkaryam, Angela Bruex, Anna C. Gilbert, John Schiefelbein, Peter J. Woolf
• Keywords: BMCBI 2010, Chips, MRNA Samples, Smart Pooling