OK James, Version 1.3.14. I subset'd MA$genes by itself, tried fit, still same error message. I then subset'd MA$M and MA$A just in case, no change - still same error message. I then regenerated the GAL file as a CSV file to be sure there were no idiosyncrasies with the way our gal files are generated, same error message on fit. One other thing, I am reading in more files than I am using in my design (i.e. I'm reading in a 100 arrays, but am only using 52 of them in the design - the remainder are for another design). Could this be the source of the error? Does limma require all arrays in the initial read-in to be used in the design? thanks S. On Jan 29, 2004, at 7:37 PM, James Wettenhall wrote: > Simon, > > It would be helpful to know which version of limma you are > using and how you read in your genelist. Did you use > RG$genes <- readGAL() ? > > Do you have any blank lines at the end of your GAL file? > > Have a look at the help for readGAL and read.table (which > readGAL calls). > > What happens if you subset your genes component of MA (or RG), > then does lmFit work? > > i.e. > > MA$genes <- MA$genes[1:16896,] > > Regards, > James > > On Thu, 29 Jan 2004, Simon Melov wrote: > >> 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 > > -- > -------------------------------------------------------------------- --- > --- > James Wettenhall Tel: (+61 3) 9345 > 2629 > Division of Genetics and Bioinformatics Fax: (+61 3) 9347 > 0852 > The Walter & Eliza Hall Institute E-mail: > wettenhall@wehi.edu.au > of Medical Research, Mobile: (+61 / 0 ) 438 527 > 921 > 1G Royal Parade, > Parkville, Vic 3050, Australia > http://www.wehi.edu.au > -------------------------------------------------------------------- --- > --- > > Simon Melov Ph.D Associate Professor & Director of Genomics Buck Institute for Age Research 8001 Redwood Blvd Novato, CA 94945 415 209 2068 Fax: 415 209 2231