Hi, read.maimages seems to be fine reading five GPR (1.3) files. But when I tried to correct for backgrond, I get this: RG <- backgroundCorrect(RG,method='normexp') Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Error in optim(c(beta, log(sigma), log(alpha)), sumloglik, gr = grsumloglik, : non-finite value supplied by optim So I ignored the background and went ahead with normalization (default one as well as loess), and did a lmFit. So far so good, but then when I tried with eBayes, I get this warning message: > fit<-eBayes(fit) Warning message: Estimation of var.prior failed - set to default value in: ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) So is there something wrong with the image files? if so, how do I know what it is? Thanks, g