Okay, thank you. On Mon, Dec 5, 2011 at 12:01 AM, Bert Gunter <gunter.ber...@gene.com> wrote: > The concentrations of the different metals within an animal are > correlated, so that doing as you suggest will almost certainly result > in nonsense P values. So I suggest you seek local statistical help or, > failing that, post on a statistical forum like stats.stackexchange.com > . > > There are various multivariate packages -- check e.g. the ChemPhys > and Multivariate task views -- that may be pertinent, but your post > suggests that you probably need some help to use them. Ergo my > suggestion above. > > Cheers, > Bert > > On Sun, Dec 4, 2011 at 7:36 AM, Kaiyin Zhong <kindlych...@gmail.com> wrote: >> 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 >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > > -- > > Bert Gunter > Genentech Nonclinical Biostatistics > > Internal Contact Info: > Phone: 467-7374 > Website: > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
-- Kaiyin Zhong ------------------------------------------------------------------------------------------------------------------ Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.