[BioC] limma, is there a limited number of levels for a factor?

[steve shen]

Hello,

Does anyone know if there is a limited number of levels for a factor  
or how to reset the defaults? I have a two factor experiment which one  
factor has 2 levels while another has 7 levels. I got errors while I  
run following analysis. Please help. Thanks,

Steve

 > design <- model.matrix(~phe+tr)
 > design
    (Intercept) pheVehicle tr1-Ant tr2-TCDD tr3-DIM tr4-Ago tr5-CH tr6- 
DMSO
1            1          0       0        0       0       0       
0        0
2            1          0       0        0       0       0       
0        0
3            1          0       0        0       0       0       
0        0
4            1          1       0        0       0       0       
0        1
5            1          1       0        0       0       0       
0        1
6            1          1       0        0       0       0       
0        1
7            1          1       0        1       0       0       
0        0
8            1          1       0        1       0       0       
0        0
9            1          1       0        1       0       0       
0        0
10           1          1       0        0       1       0       
0        0
11           1          1       0        0       1       0       
0        0
12           1          1       0        0       1       0       
0        0
13           1          1       0        0       0       1       
0        0
14           1          1       0        0       0       1       
0        0
15           1          1       0        0       0       1       
0        0
16           1          1       0        0       0       0       
1        0
17           1          1       0        0       0       0       
1        0
18           1          1       0        0       0       0       
1        0
19           1          1       1        0       0       0       
0        0
20           1          1       1        0       0       0       
0        0
21           1          1       1        0       0       0       
0        0
attr(,"assign")
[1] 0 1 2 2 2 2 2 2
attr(,"contrasts")
attr(,"contrasts")$phe
[1] "contr.treatment"

attr(,"contrasts")$tr
[1] "contr.treatment"

 > fit <- lmFit(x.data, design)
Coefficients not estimable: tr6-DMSO
Warning message:
Partial NA coefficients for 29198 probe(s)
 > fit2 <- eBayes(fit)
Warning message:
In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =  
stdev.coef.lim) :
   Estimation of var.prior failed - set to default value
 > sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_3.2.2

loaded via a namespace (and not attached):
[1] tools_2.10.1