Some code to provide some dose-viability data to play with:

FIMMdose-viability.R

library(PharmacoGx)
fimm <- downloadPSet("FIMM")
slotNames(fimm)
names(fimm@sensitivity)

head(fimm@sensitivity$info)
head(fimm@sensitivity$profiles)
fimm@sensitivity$n[1:5, 1:5]

class(fimm@sensitivity$raw)
dim(fimm@sensitivity$raw)
str(fimm@sensitivity$raw)

library(SummarizedExperiment)
rawassay <- fimm@sensitivity$raw
dim(fimm@sensitivity$profiles)
rownames(fimm@sensitivity$profiles)

getSummaryAssays <- function(pset) {
  library(reshape2)
  longfmt <- pset@sensitivity$profiles
  assaynames <- colnames(longfmt)[-1:-2]
  assaylist <- lapply(assaynames, function(x) {
    res <- dcast(longfmt, drugid ~ cellid, value.var = x)
    rownames(res) <- res[, 1]
    res <- res[,-1]
    return(res)
  })
  names(assaylist) <- assaynames
  return(assaylist)
}

getRawAssays <- function(pset){
  tmp <- getSummaryAssays(pset)[[1]]
  correctcolnames <- colnames(tmp)
  correctrownames <- rownames(tmp)
  raw <- pset@sensitivity$raw
  res <- list()
  for (i in seq_along(1:dim(raw)[2])){
    for (j in seq_along(1:dim(raw)[3])){
      tmp <- data.frame(value=raw[, i, j])
      tmp$drugid <- sub("_.+", "", rownames(tmp))
      tmp$cellid <- sub(".+_", "", rownames(tmp))
      tmp <- reshape2::dcast(tmp, drugid ~ cellid, value.var = "value")
      rownames(tmp) <- tmp[, 1]
      tmp <- tmp[, -1]
      tmp <- tmp[match(correctrownames, rownames(tmp)), match(correctcolnames, colnames(tmp))]
      res[[paste(dimnames(raw)[[2]][i], dimnames(raw)[[3]][j], sep=":")]] <- tmp
    }
  }
  return( res )
}

pset2se <- function(pset){
  myassays=c(getSummaryAssays(pset), getRawAssays(pset))
  mycoldat <- pset@cell
  rownames(mycoldat) <- mycoldat$cellid
  SummarizedExperiment(assays=myassays, colData=mycoldat)
}

pset2se(fimm)