Hello,

I'm trying to use the LIMMA package in R Studio, and am having trouble using the plotDensities command.  I am able to plot the densities of all arrays, but cannot plot the densities of select arrays using commands such as plotDensities(MA, arrays=c(1:5)).  A colleague using earlier versions of R and LIMMA was able to produce plots of individual arrays using these commands, but with the most recent version of R Studio, only a plot of all arrays appears.  Is there a way to perform this command in the latest version of R Studio?

You don't say which version of R/BioC you are using (remember to always supply the output of sessionInfo() so we know what you are using), but plotDensities() in the current version of limma doesn't have an 'arrays' argument, so that is likely the cause of your problem, rather than the fact that you are using RStudio.

Anyway, that argument is completely unnecessary. All the objects in the limma package have a '[' method, so you can just subset as if your MArrayLM object were a data.frame. So you could just do

plotDensities(MA[,1:5])

and you would get what you expect.

The plotDensities() function in the limma package has never had an 'arrays' argument. As James MacDonald explains, there is no need for it. So your colleague cannot have done what you claim.