Hello Peter, Thank you very much for the fresh approach! I will go with it to the researcher.
Thanks again, Tal ----------------Contact Details:------------------------------------------------------- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) ---------------------------------------------------------------------------------------------- On Thu, May 6, 2010 at 4:47 PM, peter dalgaard <pda...@gmail.com> wrote: > > On May 6, 2010, at 1:42 PM, Tal Galili wrote: > > > Hi Joris, > > Thank you for taking the time to answer. > > > > This data is of a test done for 39 subjects (from 2 groups) over 12 > weeks. > > And the questions I would like to answer are: > > 1) Did the test results changed over time? > > 2) Did the group effected the test results? > > 3) Did the effect of time differ for each group? > > > > I understand that the general limitation of using repeated measures anova > > here is (obviously) that even if one get's a significant "effect" of > time, > > the analysis doesn't give any clue as to how time influences the test > (the > > same goes for the interaction term). > > But a more appropriate tool would probably be some sort of GAM lm, which > is > > based on models I don't have much understanding of (yet). > > > > I am using this test since the researcher for whom I am doing the > analysis > > asked me to use it (since this is what was done in the previous work on > > similar data, done by someone else). > > > > Due to the current stage of my ignorance, and the researchers tendency > > towards this analysis - I am not sure how to proceed. > > > > You may be able to get through with anova.mlm (little-a anova) and > sphericity assumptions. However, I wouldn't trust the results. > > These data are nowhere near normally distributed, and with the size of the > data set and the pattern of many series of straight 4s, I don't think anyone > has a chance of figuring out how this affects the p-values. > > I'd rather do something like this (with the original "dat", before > jittering): > > First look at the average patterns per group: > > > aggregate(dat[-1],dat[1],mean) > DC week6 week7 week8 week9 week10 week11 > 1 control 4 4 4.000000 3.900000 3.900000 3.900000 > 2 head (20g) 4 4 3.894737 3.789474 3.736842 3.736842 > week12 week13 week14 week15 week16 week17 > 1 3.900000 3.900000 3.900000 3.850000 3.850000 3.750000 > 2 3.736842 3.684211 3.526316 3.421053 3.368421 3.315789 > > matplot(t(aggregate(dat[-1],dat[1],mean)[-1])) > > which looks promising and roughly linear. However, the slopes might differ > between subjects and this would be the appropriate variation to gauge the > mean slope differences against. So let's compute the individual slopes: > > > slope <- apply(dat[-1],1,function(x)coef(lm(x~I(1:12)))[2]) > > We can compare these between the groups with a t test: > > > t.test(slope~dat$DC) > > Welch Two Sample t-test > > data: slope by dat$DC > t = 1.6138, df = 27.189, p-value = 0.1181 > alternative hypothesis: true difference in means is not equal to 0 > 95 percent confidence interval: > -0.01217805 0.10203819 > sample estimates: > mean in group control mean in group head (20g) > -0.01800699 -0.06293706 > > However, looking more carefully at the data, we realize that many slopes > are exactly zero, so a nonparametric test might be in order. It doesn't > change anything, though: > > > wilcox.test(slope~dat$DC) > > Wilcoxon rank sum test with continuity correction > > data: slope by dat$DC > W = 232, p-value = 0.09845 > alternative hypothesis: true location shift is not equal to 0 > > Warning message: > In wilcox.test.default(x = c(-2.36672330631823e-16, -2.36672330631823e-16, > : > cannot compute exact p-value with ties > -- > Peter Dalgaard > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd....@cbs.dk Priv: pda...@gmail.com > > [[alternative HTML version deleted]] ______________________________________________ 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.