[BioC] limma subsetting issue

[Ariel Chernomoretz]

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./