Creating a scatter plot for multiple rows in R

Here is a solution with ggplot2:

The data:

dat <- read.table(text="Samp1    Samp2    Samp3     Samp4    Samp5
  Gene1    84.1     45.2     34.3      54.6     76.2
  Gene2    94.2     12.4     68.0      75.3     24.8
  Gene3    29.5     10.5     43.2      39.5     45.5", header = TRUE)

The plot:

library(ggplot2)  
ggplot(stack(dat), aes(x = ind, y = values, colour = rownames(dat))) +
  geom_point()