I want to perform some operation to the assay data of MSnSet within a MSnSetList but I think its now allowed. Could you please let me know how to do such a thing?

A simple example is shown below.

library(MSnbase)
library(pRolocdata)
data(dunkley2006)
dun <- split(dunkley2006, "replicate")
exprs(dun[[1]])[1,1] <- 1

Error in `[[<-`(`*tmp*`, 1, value = <S4 object of class "MSnSet">) :

  [[<- defined for objects of type "S4" only for subclasses of environment

Thanks.

Kamal

Yes, indeed, this doesn't work because there is no replacement method for the assayData of an item in an MSnSetList. This however seems to work

exprs(dun@x[[1]])[1,1] <- 1

It is a bit ugly, but might sort you out for now. I'll see to add proper replacement methods.

Thanks Laurent. It works.