I have assayed the concentrations of various metal elements in
different anatomic regions of two strains of mice. Now, for each
element, in each region, I want to do a t test to find whether there
is any difference between the two strains.
Here is what I did (using simulated data as an example):
# create the data frame
> elemconc = data.frame(expand.grid(id=1:3, geno=c('exp', 'wt'),
> region=c('brain', 'spine'), elem=c('fe', 'cu', 'zn')), conc=rnorm(36, 10))
> elemconc
id geno region elem conc
1 1 exp brain fe 8.497498
2 2 exp brain fe 9.280944
3 3 exp brain fe 9.726271
4 1 wt brain fe 11.556397
5 2 wt brain fe 10.992550
6 3 wt brain fe 9.711200
7 1 exp spine fe 11.168603
8 2 exp spine fe 9.331127
9 3 exp spine fe 11.048226
10 1 wt spine fe 8.480867
11 2 wt spine fe 8.887062
12 3 wt spine fe 8.329797
13 1 exp brain cu 10.242652
14 2 exp brain cu 9.865984
15 3 exp brain cu 9.163728
16 1 wt brain cu 11.099385
17 2 wt brain cu 9.364261
18 3 wt brain cu 9.718322
19 1 exp spine cu 10.720157
20 2 exp spine cu 11.505430
21 3 exp spine cu 9.499359
22 1 wt spine cu 9.855950
23 2 wt spine cu 10.120489
24 3 wt spine cu 9.526252
25 1 exp brain zn 9.736196
26 2 exp brain zn 11.938710
27 3 exp brain zn 9.668625
28 1 wt brain zn 9.961574
29 2 wt brain zn 10.461621
30 3 wt brain zn 9.873667
31 1 exp spine zn 9.708067
32 2 exp spine zn 10.109309
33 3 exp spine zn 10.973387
34 1 wt spine zn 8.406536
35 2 wt spine zn 7.797746
36 3 wt spine zn 11.127984
# use tapply to aggregate
> tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x) x)
region
elem brain spine
fe Numeric,6 Numeric,6
cu Numeric,6 Numeric,6
zn Numeric,6 Numeric,6
# check whether the order of data has been preserved after aggregation
> x['fe', 'brain']
[[1]]
[1] 8.497498 9.280944 9.726271 11.556397 10.992550 9.711200
# create an external factor for strain grouping
> tmpgeno = rep(c('exp', 'wt'), each=3)
> tmpgeno
[1] "exp" "exp" "exp" "wt" "wt" "wt"
# do the t test using the grouping factor
> x = tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x)
> t.test(x~tmpgeno) )
> x
region
elem brain spine
fe List,9 List,9
cu List,9 List,9
zn List,9 List,9
I believe I have made no mistakes so far, but I wonder is there a
better way of doing this?
--
Kaiyin Zhong
------------------------------------------------------------------------------------------------------------------
Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038
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