[BioC] Bayesian selection of genes and its correct template

[Ian Jeffery]

hi,
  I was looking at the Bayesian method of selecting genes. I used the
commands

library(limma)
fit <- lmFit(x,design=y)#x is the datafile
                        #y is the template
eb2<- eBayes(fit)
topTable(eb2,coef=,number=15,adjust="fdr")

I found that that the two groups could be defined by the template in two
ways
either
      (0,0,0,0,1,1,1,1)
or
      (-1,-1,-1,-1,1,1,1,1)
(I tryed other templates and all give one of the two gene lists)
Both methods return a gene list, so my questions are;
1. Are both methods correct?
2. If so why do they return different gene lists and what is the
significance of this?

thanks, Ian