About

MADS, which stands for Microarray Analysis of Differential Splicing, is a tool to identify differential alternative splicing by exon array. The principle of MADS is to increase the precision of exon-level and gene-level expression estimates by correcting, as much as possible, noise in observed probe intensities due to background and cross-hybridization. Our software incorporates a series of novel algorithms motivated by the “probe-rich” design of exon-tiling arrays, such as background correction, iterative probe selection and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor PTB (GSE11344). The results of this analysis are published by RNA,2008,14(8): 1470-1479.

Author

MADS is maintained by Xing Lab and Wong Lab. It is written by Yi Xing and Shihao Shen, with contributions from Karen Kapur, Hui Jiang, Zhengqing Quyang and Wing Hung Wong.

Prerequisites

1) GeneBASE

2) R

3) rpy

Source code:
     MADS_1.0.tar.gz

Feedback

Correspondences regarding the MADS algorithm should be directed to Prof.Yi Xing (yi-xing at uiowa.edu) and Prof. Wing Hung Wong (whwong at stanford.edu). Technical questions of running the MADS source code should be directed to Prof. Yi Xing (yi-xing at uiowa.edu) and Shihao Shen (shihao-shen at uiowa.edu).