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Analysis of gene expression data has emerged as an important approach to discover active pathways related to biological phenotypes. Previous pathway analysis methods use all genes in a pathway for linking it to a particular phenotype. Using only a subset of informative genes, however, could better classify samples. Here, we propose a two-stage machine learning approach for pathway analysis. During...
When proposing a new classification scheme, perhaps in the form of a classification rule or feature selection method, modelers in the bioinformatics literature typically report its performance on data sets of interest, such as gene-expression microarrays. These data sets often include thousands of features but a small number of sample points, which increases variability in feature selection and error...
The validity of a classifier depends on the precision of the error estimator used to estimate its true error. This paper considers the necessary sample size to achieve a given validity measure, namely RMS, for resubstitution and leave-one-out error estimators in the context of LDA. It provides bounds for the RMS between the true error and both the resubstitution and leave-one-out error estimators...
Genotyping quality is one of the key properties that defines the success chances of any genome-wide association studies. Data cleaning of the genotype data is therefore an important part of the statistical analysis. With family-data the genotype quality of each study subject can be assessed globally, using genome-wide family-based association test. We applied the approach to different, commonly used...
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