[BioC] eBayes giving warning, should I trust the result?

[Guoneng]

Hi,

Here is my code (thanks to all those who helped me with getting the 
columns right).

library(limma)
targets <- readTargets('targets.txt')
f <- function(x) as.numeric(x$Flags > -99)
RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F532 
Median",Gb="B532 Median",Rf="F635 Media
n",Rb="B635 Median"))  
RG$printer <- getLayout(RG$genes)
MA <- normalizeWithinArrays(RG)
design <- modelMatrix(targets,ref="Reference")
fit<-lmFit(MA,design)
fit<-eBayes(fit)

After the last line I get this warning:
Warning message:
Estimation of var.prior failed - set to default value in: ebayes(fit = 
fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim)

To make it even more unnerving is that when I typed "fit" to see what is 
in there, all the Ref values are NA (in the targets.txt file, I assigned 
Exp and Ref to various channels).

Should I be worried about these NULL values and the warning message?

Thanks again!
G