R/median.raw.R

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

`median.raw` <-
function(x){
         
         element1 <- c(NULL)
         element2 <- c(NULL)
         element3 <- c(NULL)
         replis <- unique(x[[4]][,"ID"])
            for (i in seq(along=replis)) {
               sample.lines <- which(x[[4]][,"ID"]==replis[i])
               sample.mtx <- x[[1]][sample.lines,]
               medians <- apply(sample.mtx,2,median)
               element1 <- rbind(element1,medians)
               mads <- apply(sample.mtx,2,mad)
               element2 <- rbind(element2,mads)
               element3 <- rbind(element3,x[[4]][sample.lines[1],])
            }
         rownames (element1) <- c(1:nrow(element1))
         rownames (element2) <- c(1:nrow(element1))
         rownames (element3) <- c(1:nrow(element1))
         data.list <- list(sample.medians=element1,
                           sample.mads=element2,
                           array.description=x[[3]],
                           data.annotation=element3)
         return (data.list)
}