Thanks for the response, Carsten!
I tried your code, and while I could get it to work with the first mass feature listed in the groups, I couldn't get it to work with any others. For example, I tried looking at the 4th mass feature, and I got an error that says, "Error in tempsplit[[2]] : subscript out of bounds".
Here's what I did for the 1st mass feature (and this worked):
MF1.raw <- getEIC(set5.filledpeaks, rt="raw", groupidx=1)
MF1.cor <- getEIC(set5.filledpeaks, rt="corrected", groupidx=1)
par(mfrow=c(2,1))
plot(MF1.raw, set5.filledpeaks, groupidx=1)
plot(MF1.cor, set5.filledpeaks, groupidx=1)
And here's what I did for the 4th mass feature (and this gave me that error above when I tried getEIC so I didn't even get to the plot part):
MF4.raw <- getEIC(set5.filledpeaks, rt="raw", groupidx=4)
MF4.cor <- getEIC(set5.filledpeaks, rt="corrected", groupidx=4)
Any suggestions? Thank you very much for your help!
Laura