[BioC] lmFit Error: "comparison of these types is not implemented"

[Jose Rodriguez]

I get the following error after executing the following command (using 
limma package for microarray analysis):

 > fit3< lmFit(subGeneIDMatrix[,c(2:3,16:17)],design)
Error in fit3 < lmFit(subGeneIDMatrix[, c(2:3, 16:17)], design) :
  comparison of these types is not implemented

The columns of the matrix I refer to are log transformed expression 
sets. The design matrix is simple:
 > design
       A      B
1      1       0
2      1       0
3      0       1
4      0       1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$`factor(c(1, 1, 2, 2))`
[1] "contr.treatment"

These two sets of data I am trying to compare are part of a larger 
experiment in which the error does not show up. Could the error be a bug 
or does it have something to do with the quality of this particular data 
subset?
Thanks!