Gene Selection Using GeneSelectMMD

This document demonstrates how to use the GeneSelectMMD package to detect significant genes and to estimate false discovery rate (FDR), false non-discovery rate (FNDR), false positive rate (FPR), and false negative rate (FNR), for a real microarray data set based on the method proposed by Qiu et al. (2008). It also illustrates how to visualize the fit of the model proposed in Qiu et al. (2008) to the real microarray data set when the marginal correlations among subjects are zero or close to zero. The GeneSelectMMD package is suitable for the case where there are only two tissue types and for the case where tissue samples within a tissue type are conditionally independent given the gene (c.f. Qiu et al., 2008).