R/msecalc.R

In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

msecalc <- 
function (eS, lam, alpha, lowessnorm, R) 
{
    starttime <- Sys.time()
    mat1 <- as.matrix(exprs(eS))
    mat2 <- as.matrix(mat1)

    n <- dim(mat2)[2]
    p <- dim(mat2)[1]
    mat2 <- jggrad2(mat2, lam, alpha)
    if (lowessnorm) {
        mat2l <- lnorm(mat2[, (n + 1):(2 * n)])
        mat2a <- lnorm(mat2[, (2 * n + 1):(3 * n)])
        mat2 <- lnorm(mat2[, 1:n])
    }
    else {
        mat2l <- norm(mat2[, (n + 1):(2 * n)])
        mat2a <- norm(mat2[, (2 * n + 1):(3 * n)])
        mat2 <- norm(mat2[, 1:n])
    }

    yres <- R %*% t(mat2)
    ylres <- R %*% t(mat2l)
    yares <- R %*% t(mat2a)
    r1 <- sum(yres^2)
    r2 <- sum(2 * yres * ylres)
    r3 <- sum(2 * yres * yares)

    return(c(r1, r2, r3))
}