Dear Ariel, Thanks for pointing out this problem. In limma 2.7.12 (on Bioconductor devel now) the design matrix is no longer subsetted when an MArrayLM is subsetted. Best wishes Gordon > Date: Sat, 02 Sep 2006 09:13:24 -0300 > From: Ariel Chernomoretz <ariel at="" df.uba.ar=""> > Subject: [BioC] limma subsetting issue > To: "'Bioconductor'" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <44F97564.7080007 at df.uba.ar> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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./