Isoqqstat(x, y, fudge, niter)
IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2/1.
isoreg
, Isoallfdr
, IsoGenemSAM
Isoqval
,IsoTestSAM
,IsoSAMPlot
set.seed(1234)
x <- c(rep(1,3),rep(2,3),rep(3,3))
y1 <- matrix(rnorm(4500, 1,1),500,9) ## 500 genes with no trends
y2 <- matrix(c(rnorm(1500, 1,1),rnorm(1500,2,1),
rnorm(1500,3,1)),500,9) ## 500 genes with increasing trends
y <- data.frame(rbind(y1, y2)) ##y needs to be a data frame
qqstat <- Isoqqstat(x, y, fudge="pooled", niter = 50)
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