Hello My name is Morten and I am a newbee. Using R 1.9.1 and limma 1.7.8. I have some trouble in getting the layout for a GenePix GAL file supplied from Axon Instruments. > gal <- readGAL() > layout <- getLayout(gal) Error in getLayout.default(gal) : number of grid columns is not 4 the final line in my GAL file looks like this: 1 105 215 Pro25G (+)Pro25G-03 1 pos Pro25G NA Im stuck:( morten

> Hello > > My name is Morten and I am a newbee. Using R 1.9.1 and limma 1.7.8. You are not using limma 1.7.8. Type packageDescription("limma") to see what version you really have. > I have some > trouble in getting the layout for a GenePix GAL file supplied from Axon > Instruments. > >> gal <- readGAL() >> layout <- getLayout(gal) > Error in getLayout.default(gal) : number of grid columns is not 4 > > the final line in my GAL file looks like this: > 1 105 215 Pro25G (+)Pro25G-03 1 pos Pro25G NA The purpose of getLayout() is to get the print tip layout. You have data from an Agilent array, although you don't tell us, and Agilent doesn't use print tips. So you don't actually need to set the print layout at all. If you really were using limma 1.7.8, it would have set layout <- list(ngrid.r=1,ngrid.c=1,nspot.r=105,nspot.c=215) As it is, the error message does correctly warn you that there isn't a grid structure. Gordon > Im stuck:( > morten