[BioC] changes in targets frame (EdgeR)

[anna [guest]]

Hello everybody,
I would like to use section "3.5 Comparisons Both Between and Within Subjects" of the user's guide but try with disease 1 and 2 as one group.
So it would be 6 healthy patients, and 12 with Disease.
Can anybody help me re-number the patients in the targets frame ?
I would like also to try keeping the 3 groups, but remove one outlier,so in the last disease groups there would be only 2 patients.
thank you for your help !
anna

originlally it was like this:
> targets
Disease Patient Treatment
1 Healthy 1 None
2 Healthy 1 Hormone
3 Healthy 2 None
4 Healthy 2 Hormone
5 Healthy 3 None
6 Healthy 3 Hormone
7 Disease1 4 None
8 Disease1 4 Hormone
9 Disease1 5 None
10 Disease1 5 Hormone
11 Disease1 6 None
12 Disease1 6 Hormone
13 Disease2 7 None
14 Disease2 7 Hormone
15 Disease2 8 None
16 Disease2 8 Hormone
17 Disease2 9 None
18 Disease2 9 Hormone

> Patient <- gl(3,2,length=18)
> Disease <- factor(targets$Disease, levels=c("Healthy","Disease1","Disease2"))
> Treatment <- factor(targets$Treatment, levels=c("None","Hormone"))
> data.frame(Disease,Patient,Treatment)
Disease Patient Treatment
1 Healthy 1 None
2 Healthy 1 Hormone
3 Healthy 2 None
4 Healthy 2 Hormone
5 Healthy 3 None
6 Healthy 3 Hormone
7 Disease1 1 None
8 Disease1 1 Hormone
9 Disease1 2 None
10 Disease1 2 Hormone
11 Disease1 3 None
12 Disease1 3 Hormone
13 Disease2 1 None
14 Disease2 1 Hormone
15 Disease2 2 None
16 Disease2 2 Hormone
17 Disease2 3 None
18 Disease2 3 Hormone
> design <- model.matrix(~Disease+Disease:Patient+Disease:Treatment)



 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

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

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