Dear list:

I have 13 pairs of samples (pre and post-treatment) and I want to see 
witch pathways are affected by treatment. My phenoData is like this:

	Treatment 	Pairs
1 	Pre 	1
2 	Post 	1
3 	Pre 	2
4 	Post 	2
5 	Pre 	3
6 	Post 	3
7 	Pre 	4
8 	Post 	4
9 	Pre 	5
10 	Post 	5
11 	Pre 	6
12 	Post 	6
13 	Pre 	7
14 	Post 	7
15 	Pre 	8
16 	Post 	8
17 	Pre 	9
18 	Post 	9
19 	Pre 	10
20 	Post 	10
21 	Pre 	11
22 	Post 	11
23 	Pre 	12
24 	Post 	12
25 	Pre 	13
26 	Post 	13

I try to use Pairs as the co-factor for treatment to run globaltest like 
this and got an error message:
 > gt.kegg.pairs.treat <- globaltest(data, Treatment ~ factor(Pairs), kegg)
Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("01.01.Pre",  :
        invalid 'dimnames' given for data frame
If I just run:
 > gt.kegg.pairs.treat <- globaltest(data, Treatment, kegg)
or:
 > gt.kegg.pairs.treat <- globaltest(data, factor(Pairs), kegg)
I don't have get any errors.

Could somebody point out what is the problem here?

Thanks,
Xia







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