On Wed, Dec 14, 2011 at 5:09 AM, Esther Robinson <
esther.robinson@sjc.ox.ac.uk> wrote:

> 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
>

Hi, Esther.

The first argument to geneSetTest is an index vector and is used to select
the values from the statistics argument.  You have used a numeric vector.
 Take a look at the help for geneSetTest a bit more closely and then get
back to us with questions.

Sean



> I expect i am doing something simple wrong. Any help would be appreciated.
> Thank you,
> Esther Robinson
>
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