Simple and flexible classification of gene expression microarrays via Swirls and Ripples

Background: A simple classification rule with few genes and parameters is desirable when applying a classification rule to new data. One popular simple classification rule, diagonal discriminant analysis, yields linear or curved classification boundaries, called Ripples, that are optimal when gene expression levels are normally distributed with the appropriate variance, but may yield poor classification in other situations. Results: A simple modification of diagonal discriminant analysis yields smooth highly nonlinear classification boundaries, called Swirls, that sometimes outperforms Ripples. In particular, if the data are normally distributed with different variances in each class, Swirls substantially outperforms Ripples when using a pooled variance to reduce the number of parameters. The proposed classification rule for two classes selects either Swirls or Ripples after parsimoniously selecting the number of genes and distance measures. Applications to five cancer microarray data...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Stuart G. Baker
• Keywords: BMCBI 2010, Classification Rule, Diagonal Discriminant Analysis, Simple Classification Rule