synlet (version 1.2.2)

tTest: student's t-test basing on B-score

Description

Select hits by student's t-test using B-score from treatment and control plates.

Usage

tTest(masterPlate, bScore, numTreat, numCont)

Arguments

masterPlate

the master plate to be analyzed

bScore

normalized bScore

numTreat

number of treatment plates

numCont

number of control plates

Value

• A list containing student's t-test for each master plate
  • pvalue: p-value of the t-test
  • Treat_Cont: difference in bscore: treatment - control
  • p_adj: BH adjusted p-value

References

Birmingham, A. et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 6, 569-575 (2009).

Examples

bscore.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)), bScore,
  exampleDat, control = "control", treatment = "treatment", simplify = FALSE)
bscore.ttest  <- sapply(names(bscore.res), tTest, bscore.res, numTreat = 3,
  numCont = 3, simplify = FALSE, USE.NAMES = TRUE)
bscore.combined <- data.frame(do.call(rbind, lapply(names(bscore.ttest),
  function(x) if (!is.null(bscore.ttest[[x]])) {data.frame(MASTER_PLATE = x,
  siRNAs = rownames(bscore.ttest[[x]]), bscore.ttest[[x]])})))