Potential bias in GO::TermFinder.
The increased need for multiple statistical comparisons under conditions of non-independence in bioinformatics applications, such as DNA microarray data analysis, has led to the development of alternatives to the conventional Bonferroni correction for adjusting P-values. The use of the false discovery rate (FDR), in particular, has grown considerably. However, the calculation of the FDR frequently depends on drawing random samples from a population, and inappropriate sampling will result in a bias in the calculated FDR. In this work, we demonstrate a bias due to incorrect random sampling in the widely used GO::TermFinder package. Both T(2) and permutation tests are used to confirm the bias for a test set of data, which leads to an overestimation of the FDR of about 10%. A simple fix to the random sampling method is proposed to remove the bias.
Flight
Robert M
RM
Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada.
Wentzell
Peter D
PD
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012984:Software