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I have data with three factors with three replicates and I want to make pairwise mean comparisons. One way is to do Tukey Posthoc test for mean comparison which I am able to do after one way Anova. but I cannot figure out which test to use for multiple factor data. after calculating the pairwise mean significant differences I want to put the significance symbols on line chart in ggplot2. Any Ideas

example data
Gene    Treatment   Time    replicate   expression
gene1   10°C    3   1   0.125132183
gene1   10°C    3   2   0.107514407
gene1   10°C    3   3   0.09159049
gene2   10°C    3   1   0.060833328
gene2   10°C    3   2   0.055756875
gene2   10°C    3   3   0.049362816
gene1   10°C    6   1   0.332224339
gene1   10°C    6   2   0.325728753
gene1   10°C    6   3   0.375734111
gene2   10°C    6   1   0.222602764
gene2   10°C    6   2   0.208011959
gene2   10°C    6   3   0.285778295
gene1   18°C    3   1   0.411072664
gene1   18°C    3   2   0.326374874
gene1   18°C    3   3   0.353573578
gene2   18°C    3   1   0.458390686
gene2   18°C    3   2   0.384614136
gene2   18°C    3   3   0.451072275
gene1   18°C    6   1   0.333687974
gene1   18°C    6   2   0.349928428
gene1   18°C    6   3   0.271766252
gene2   18°C    6   1   0.433498867
gene2   18°C    6   2   0.645699271
gene2   18°C    6   3   0.444076527
ashar14
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  • for the ggplot question, see here : http://stackoverflow.com/questions/17084566/put-stars-on-ggplot-barplots-and-boxplots-to-indicate-the-level-of-significanc You should show some code, we cannot guess what variables you want plotted – scoa Aug 22 '15 at 05:46
  • @ashar14 - It's a bit unclear what your problem is. Are you unsure which type of test to use? Or do you know which test you'd like to use but are having trouble finding a way to code it in R? – scribbles Aug 24 '15 at 04:33

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