tTest {synlet} | R Documentation |
Select hits by student's t-test using B-score from treatment and control plates.
tTest(masterPlate, bScore, numTreat, numCont)
masterPlate |
the master plate to be analyzed |
bScore |
normalized bScore |
numTreat |
number of treatment plates |
numCont |
number of control plates |
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
Birmingham, A. et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 6, 569-575 (2009).
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]])})))