R : Error in " " : incorrect number of dimensions , when using intersect

Question

So I am basically trying calculate diffrences between datasets, but for some reason I receive the following error:"Error in expr1[overlap, ]: incorrect number of dimensions It might be very simple but I can't seem to fix it.

I am reading 4 .RData files.They all contain the dataframe Expr which has around 54000 rows and 10 columns with data. All files have the same column names but the rows names are not the same but for a big part they are so by using intersect I calculate the overlap but somehow this doesn't work as it should.

Example of the files:

file1:
               GSM10     GSM11
    1007_s_at  7.777639  8.582393
    1053_at    9.029875  7.937305
    117_at     7.026750  6.271279
    121_at     7.800896  7.842556
    1255_g_at  3.472406  3.486788
    1294_at    6.332505  6.176560

file2:
               GSM10     GSM11
    1007_s_at  8.471424  9.499584
    1053_at    9.047367  7.981026
    1255_g_at  4.231098  4.226397
    1294_at    7.482370  7.289183

Thanks in advance!!

Part of the code:

data <- list()
load("file1")  
data$old_fRMA <- expr
load("file2") 
data$old_PMfRMA <- expr   
#runTimeInfo
load("file3") 
data$new_PMfRMA <- expr   
load("file3") 
data$new_fRMA <- expr

##
compare.fRMA <-
  function(expr1, expr2, no_duplicate_probeset = no_duplicate_probeset) {
    overlap <- intersect(rownames(expr1), rownames(expr2))
    expr1 <- expr1[overlap,]
    expr2 <- expr2[overlap,]

    datalength <- length(colnames(expr1))
    difference <-
      sapply(1:datalength, function(x)
        abs(expr1[x] - expr2[x]))
    difference.max <- sapply(difference, max)
    difference.mean <- sapply(difference, mean)

    out <- list()
    #### All probesets ####
    out$maxall <- max(difference.max)
    out$meanall <- mean(difference.mean)

    #################
    expr1 <- expr1[no_duplicate_probeset,]
    expr2 <- expr2[no_duplicate_probeset,]

    difference <-
      sapply(1:datalength, function(x)
        abs(expr1[x] - expr2[x]))
    difference.max <- sapply(difference, max)
    difference.mean <- sapply(difference, mean)

    #### TG probesets ####
    out$maxTG <- max(difference.max)
    out$meanTG <- mean(difference.mean)
    return(out)
  }

res <- list()
for (i in 1:4) {
  res[i] <- list()
  for (j in (i + 1):4) {
    if (j>4) { break()

    }
    # print(paste(i,j ,sep=","))
    res[i][j] <- compare.fRMA(data[i], data[j])

  }
}