Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit

Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit

MOTIVATION Genomic DNA was hybridized to oligonucleotide microarrays to identify single-feature polymorphisms (SFP) for Arabidopsis, which has a genome size of approximately 130 Mb. However, that method does not work well for organisms such as barley, with a much larger 5200 Mb genome. In the present study, we demonstrate SFP detection using a small number of replicate datasets and complex RNA ...

Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays

MOTIVATION Oligonucleotide arrays such as Affymetrix GeneChips use multiple probes, or a probe set, to measure the abundance of mRNA of every gene of interest. Some analysis methods attempt to summarize the multiple observations into one single score before conducting further analysis such as detecting differentially expressed genes (DEG), clustering and classification. However, there is a risk...

Detecting multivariate outliers using projection pursuit with particle swarm optimization

Detecting outliers in the context of multivariate data is known as an important but difficult task and there already exist several detection methods. Most of the proposed methods are based either on the Mahalanobis distance of the observations to the center of the distribution or on a projection pursuit (PP) approach. In the present paper we focus on the one-dimensional PP approach which may be...

High Dimensional Feature Reduction via Projection Pursuit

................................................................................................................................... v 1 . INTROIIUCTION .................................................................................................................... 1 1.1 Background .............................................................................................................. ...

Feature Extraction with Supervised Projection Pursuit