Bioconductor RankProd Package Vignette

The RankProd package contains functions for the analysis of gene expression microarray data, in particular the identification of differentially expressed genes. RankProd utilizes the so called rank product non-parametric method (Breitling et al., 2004, FEBS Letters 573:83) to identify up-regulated or down-regulated genes under one condition against another condition, e.g. two different treatments, two different tissue types, etc. Rank Product is a non-parametric statistic that detects items that are consistently highly ranked in a number of lists, for example genes that are consistently found among the most strongly upregulated genes in a number of replicate experiments. It is based on the assumption that under the null hypothesis that the order of all items is random the probability of finding a specific item among the top r of n items in a list is p = r n . Multiplying these probabilities leads to the definition of the rank product RP = ∏ i ri ni , where ri is the rank of the item in the i-th list and ni is the total number