Dear Jose, My suggestion: don't remove the empty spots in the first place. Best wishes Gordon > Date: Mon, 2 Mar 2009 09:48:48 -0600 > From: Jose Coria <com90185 at="" gmail.com=""> > Subject: [BioC] limma printer layout > To: bioconductor at stat.math.ethz.ch > > I'm trying to plot background intensity after clean empty values. When I > check the information through layout, I got ngrid.r=12, ngrid.c=4, > nspot.r=25, nspot.c=24 (28800 spots) > Cleaning empty data I have 27003 spots., searching in forum I found this > suggestion: > > Dear Vanessa, >> >> limma always assumes complete print-tip-groups, so the only way to >> use imageplot() correctly is to complete your arrays by putting back >> >> to last 4 spots of each print-tip-group as NA. You can do this by: >> >> narrays <- ncol(RG_e1) >> Y <- matrix(NA,21632,narrays) >> RG <- new("RGList",list(R=Y,G=Y,Rb=Y,Gb=Y) >> RG$printer <- RG_e1$printer >> >> missingspots <- spotr(RG$printer)==26 & spotc(RG$printer)>=23 >> RG$R[!i,] <- RG_e1$R >> RG$Rb[!i,] <- RG_e1$Rb >> RG$G[!i,] <- RG_e1$G >> RG$Gb[!i,] <- RG_e1$Gb >> >> Best wishes >> >> Gordon >> >> but If i try to follow the commands I have this error message: > > missingspots <- spotr(RG1$printer)==26 & spotc(RG1$printer)>=23 > Error en 1:layout$nspot.r : Argumento NA/NaN > Can anyone suggest me something? > Thanks > > -- > Jos? Antonio Coria Fern?ndez > Universidad Nacional Auton?ma de M?xico > Facultad de Estudios Superiores Acatl?n > Centro de Desarrollo Tecnol?gico > (Departamento Servicios de C?mputo) > Av. Alcanfores y San Juan Totoltepec S/N > C.P. 53150 Tel: 56 23 17 62, 56 23 15 07 > Cubiculo 114 Planta Alta > email: com90185 at gmail.com, > jcoriafdz at hotmail.com > > (_)(_) > (,,) > =()= > ((__)\ > _|L\_______/ > The Lab Rat