[R] multiple comparisons on a between factor

[elgoran at web.de]

   Dear list,
   im facing an issue of statistical data analysis that I consider myself
   unable to resolve in R so i hope to get some valuable insights from you. i
   run an ANOVA with four factors; factor4 is an between factor (two different
   groups measured), the others are withins (tested across /all/ subjects).
   accordingly, my model looks as follows:
   fm1
   <-aov(dataSubjects~(factor1*factor2*factor3*factor4)+Error(subject/(factor1*
   factor2*factor3))+factor4,data=mydata)
   print(summary(fm1))
   so  far so good. i now would like to perform multiple comparisons, but
   separately for each level of factor4 (two). this is how I do it: i sort out
   (using subset) the levels im interested in comparing, say level 1 of factor
   1
   Type.lvl1 <- subset(mydata, factor1 == "lvl1")
   and then compute an uncorrected pairwise t-test between the two levels of
   factor 4:
   Type.lvl1.P<-pairwise.t.test(Type.lvl1$dataSubjects,Type.lvl1$factor4,p.adj
   = "none")
   i do this for every comparison im interested in and apply any method for
   multiple comparison correction afterwards on the entire set of p values
   obtained. is this valid (in statistical terms)? if not, could anyone refer
   to a better procedure i should use instead?
   Thanks in advance.
   Lisa

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