Getting an error from a function when the input data is clearly wrong does not constitute a bug in the software. The latest versions of limma set the 'genes' component directly from the gpr files. This means that there is no longer any need to read the GAL file with GenePix data. I suggest that you stop using your GAL file which for some reason does not match your gpr files. Gordon > Hi, > this may be my ignorance, but I am persistently getting an error upon > reading in one data set. It seems to be in the implementation of the > gene list in the normalized MA. > > The error I am getting after trying to fit is.. > > > fit <- lmFit(MA, design) > Error: (subscript) logical subscript too long > > After checking the size of M,A, and the gene list in MA, its clear that > M and A are the correct size. But for some reason, the genelist is > incorrectly sized however you look at it (which is not the case in the > input gpr files..) > > show(MA) > An object of class "MAList" > $genes > Block Row Column ID Name > 1 1 1 1 Human Cot 1 Human Cot 1 > 2 1 1 2 Spot Report Product 2 Spot Report Product 2 > 3 1 1 3 B-Human Actin B-Human Actin > 4 1 1 4 Buffer Buffer > 5 1 1 5 Poly A Poly A > 16891 more rows ... > > > MA$M[16891:16896,] > MB12A04 MB12A05 ect.. > [1,] -0.08841763 -0.24117406 > [2,] -0.01282521 -0.09876827 > [3,] 0.16414844 0.44696644 > [4,] 0.26038965 0.51199616 > [5,] 0.28553731 -0.51235751 > [6,] 0.03343551 0.31066801 > > > MA$M[16894:16897,] > Error: subscript out of bounds > > This is fine, as there are only 16896 rows. > > But for the MA$genes.. > > MA$gen[16894:16897,] > Block Row Column ID Name > 16894 32 22 22 Spot Report Product 8 Spot Report Product 8 16895 > 32 22 23 Buffer Buffer 16896 32 > 22 24 Buffer Buffer NA NA NA > NA <na> <na> > > MA$gen[16894:16898,] > Block Row Column ID Name > 16894 32 22 22 Spot Report Product 8 Spot Report Product 8 16895 > 32 22 23 Buffer Buffer 16896 32 > 22 24 Buffer Buffer NA NA NA > NA <na> <na> NA.1 NA NA NA > <na> <na> > > MA$gen[16894:16899,] > Block Row Column ID Name > 16894 32 22 22 Spot Report Product 8 Spot Report Product 8 16895 > 32 22 23 Buffer Buffer 16896 32 > 22 24 Buffer Buffer NA NA NA > NA <na> <na> NA.1 NA NA NA > <na> <na> NA.2 NA NA NA > <na> <na> > > and so on. > > Is this why I'm getting the fit error listed above, ie is this a bug? > > Simon

Thanks Gordon... Actually that wasn't the problem (input data wrong as you suggested). The problem was I was reading in more files than I was using. As far as I can tell, limma requires the same number of files you initially read in to match the numbers of arrays in the target file. I read in over a 100 arrays, then only described 50 of them in my targets file (intending to use the other 50 later). I kept getting the error I mentioned, but finally figured out that unless your target file matches the number of arrays initially read in, then you will get an error. Once I eliminated the excess arrays, they read in fine (i.e. matched the target file with the number of arrays read in). Maybe this is my ignorance, but this might be worth explicitly mentioning in the guide (unless I am misinterpreting my fix). Any word on the addition of the technical rep and biological rep feature you mentioned in your post from September last year? I have been treating the technical reps as biological reps, but it would be really useful to explicitly handle this via a function within limma. Thanks again, Simon.