[BioC] error message in GeneSetTest in limma

[Esther Robinson]

Hello,
I am a very new user of R and hope you can help. I have tried the fora and online help. I am using limma to analyse microarray data.
I have run into a problem with GeneSetTest which i don't understand, but think it is something to do with my input data. My whole data set has 18296 rows of t values.
I have created a separate subset for the genes on an ICE whose t values I want to compare in Gene Set Test. Some of these values are negative as is expected with t values.
The small dataset is seen below
> sub.2
 [1] -1.628088679  1.199633873  0.652152009  3.214887735  3.233349792
 [6]  2.362553469  3.525487896  4.940010275  4.897654582 -0.002203589
[11]  1.845625471  1.561264994  7.507653938 17.546755720  7.080742224
[16] -0.025233341  2.410513643  1.083376106  1.908051944  1.112365831
[21]  0.564130982  1.709511634 10.066341340 12.229110920  5.529650005
[26]  1.701063357  2.229950100  2.721246420  5.390680871  3.722832322
[31]  4.796353818  3.525246899  4.822326403 -4.002596576  0.835416155
[36]  2.537629585  1.991560632 -0.041158816  0.802931410 -1.869976733
[41]  0.238770948 -1.052793736 -0.553059499 -0.023182488

The whole array data is designated sub.3 of my data table and I have checked this contains only numeric characters ( and when run with a dummy "sel" set is fine)
when I run this:
library(limma)
> sel<-sub.2
> stat<-sub.3
> geneSetTest(sel, stat, alternative="up")
Error in statistics[selected] : 
  only 0's may be mixed with negative subscripts
I expect i am doing something simple wrong. Any help would be appreciated.
Thank you,
Esther Robinson