When I enter RSS$scan.mat in the console window, I just get a summary message. How do I see the raw numbers?

Here's how to manipulate the extmats:

• convert to a regular R matrix using empty brackets:

x <- RSS$scan.mat[]   ## x receives a copy of the whole scan as a normal R matrix

• show some of the data by indexing, which converts to a normal R matrix and prints the result:

RSS$scan.mat[1:10, 15:20]  ## prints samples 1 through 10 of pulses 15 through 20

• modify some of the data by indexed assignment:

RSS$scan.mat [300:350,] <- 252     ## paint a white ring into the raw data buffer
gui.update.plot.window()           ## scan convert the new raw data and display it

• get the dimensions of the data using the dim() function, just as for an R matrix:

dim(RSS$scan.mat)

• extract scores for a blip by matrix indexing:

blip.sample <- c(100, 100, 101, 101, 102, 102, 102, 103)   ## radial coordinates of samples in blipblip.pulse  <- c(222, 223, 223, 224, 225, 226, 227, 227)                  ## angular coordinates of samples in blip
blip.data <- RSS$score.mat[cbind(blip.sample, blip.pulse)] ## cbind creates an indexing matrix

So blip.data now holds the raw data for (sample 100, pulse 222), (sample 100, pulse 223), sample(101, pulse 223) and so on.