Surrogate variable analysis(SVA) to correct the unknown batch effects

Usage

svacor(xset, lv = NULL, method = "medret", intensity = "into")

Arguments

xset: xcmsset object
lv: group information
method: parameter for groupval function
intensity: parameter for groupval function

Value

list object with various components such raw data, corrected data, signal part, random errors part, batch part, p-values, q-values, mass, rt, Posterior Probabilities of Surrogate variables and Posterior Probabilities of Mod. If no surrogate variable found, corresponding part would miss.

Details

this is used for reviesed version of SVA to correct the unknown batch effects

Examples

if (FALSE) { # \dontrun{
library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(cdffiles)
xset <- group(xset)
xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
xset2 <- group(xset2, bw = 10)
xset3 <- fillPeaks(xset2)
df <- svacor(xset3)
} # }