synlet (version 1.2.2)

rankProdHits: Select hits by the rank product method

Description

Select hits by rank product methods by comparing treatment and control.

Usage

rankProdHits(masterPlate, dat, treatment, control, normMethod = "PLATE")

Arguments

masterPlate

the master plate to be analyzed

dat

synthetic lethal RNAi screen data

treatment

the treatment condition in EXPERIMENT_MODIFICATION

control

the control condition in EXPERIMENT_MODIFICATION

normMethod

normalization methods to be used. If "PLATE", the raw readouts are normalized by plate median, otherwise use provided control siRNA

Value

• A list contains results by the rank product method for each master plate.
  • MASTER_PLATE: location of siRNA
  • pvalue_treat_lowerthan_cont: p-value for the hypothesis that treatment has lower normalized readout compared to control
  • FDR_treat_lowerthan_cont: FDR value
  • treat_cont_log2FC: log2 fold change of treatment / control

References

Breitling, R., Armengaud, P., Amtmann, A. & Herzyk, P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573, 83-92 (2004).

Hong, F. et al. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 22, 2825-2827 (2006).

Examples

rankp.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)),
  rankProdHits, exampleDat, control = "control", treatment = "treatment",
  simplify = FALSE)
rankp.c <- data.frame(do.call(rbind,
  lapply(names(rankp.res), function(x) rankp.res[[x]])))