Dear Gordon and BioC users, I have recently updated R and BioC packages (R.2.3.0 and limma 2.7.9) and found the following issue when I try to subset a MArrayLM object. "f" is a MArrayLM object obtained using 'contrasts.fit' and > class(f) [1] "MArrayLM" attr(,"package") [1] "limma" > dim(f$contrasts) #lot of contrasts [1] 8 21 > dim(f$coef) [1] 10984 21 > class(f[,c(1,4,8)]) #subsetting columns 1:8 runs smoothly [1] "MArrayLM" attr(,"package") [1] "limma" > class(f[,9]) #subsetting any column between 9 - 21 does not work Error in "[.MArrayLM"(f, , 9) : subscript out of bounds I think the problem relies on how subsetting works on the design matrix of the MArrayLM object (which in my case has 8 columns) Under R.2.21 and limma 2.4.7 this was not an issue (almost). The following warning was raised: "Warning message: design matrix is singular" but the subsetting operation was performed anyway. I know that from the point of view of the MArrayLM object integrity this is not the ideal behavior, but it proved to be really usefull (at least for me). If this new behavior is limma's responsability, and not R's, may I suggest to change things in orther to allow subsetting using all contrasts again? Thanks Best Ariel./