a <- c(1, 2, 3, 4)
b <- c(5, 6, 7, 8)
c <- c(9, 10, 11, 12)
d <- data.frame(a, b, c)
d <- t(d)`

require(xlsx)
require(XLConnect)
SampleSetNumber <- 0     # 0 = First sample set, 1 = second...
AppendData <- SampleSetNumber*3
wb <- loadWorkbook("NewWorkbook.xlsx", create=T)
createSheet(wb, name = "Data")
writeWorksheet(wb, d, sheet="Data", header=F, startRow = AppendData+(2:4), startCol=1, rownames=NULL)
saveWorkbook(wb, "NewWorkbook.xlsx")

SampleSetNumber <- 0       # Rows 2:4
SampleSetNumber <- 1       # Rows 5:7... so on