On Fri, May 20, 2005 2:29 am, M Perez said: > Thanks Gordon for all your answers. > > I am afraid I have more questions, now about "normexp" > background correction, I am trying to use "normexp" > with Limma 1.8 and I got this error > >> RG <- backgroundCorrect(RG, method="normexp", > offset=100); > Corrected array 1 > Corrected array 2 > Error in optim(theta, m2loglik.normexp, control = > list(trace = trace), : > Function cannot be evaluated at initial parameters > > Note that only the two first files are corrected for > background the third file seem to have something > wrong, but when I try with Limma 1.96 and I got this > new error: > >>RG <- backgroundCorrect(RG, method="normexp", > offset=100); > Corrected array 1 > Error in optim(c(beta, log(sigma), log(alpha)), > sumloglik, gr = grsumloglik, : > initial value in 'vmmin' is not finite We are working on this bug now. In the meantime, try this: RG2 <- backgroundCorrect(RG,method="subtract") RG2$Gb <- RG2$Rb <- array(0,dim(RG2)) RG3 <- backgroundCorrect(RG2,method="normexp",offset=100) In principle, this is the same as what you've asked for, but it seems to get around a bug. Gordon > Now just only the first file could be corrected using > "normexp", I think this problem show up because of the > nature of my files that they are "ScanArray" format > files, as I read in other posts "normexp" works most > of the time but not on > all data sets but I would like to know if is possible > to do something before to try the "half" correction. > Any idea what could be the reason of these errors? > Thank you in advance. > Manuel