[R] R Anova Analysis

[Yanwei Tan]

Dear all,

I have a quite basic questions about anova analysis in R, sorry for 
this, but I have no clue how to explain this result.

I have two datasets which are named: nmda123, nmda456. Each dataset has 
three samples which were measured three times. And I would like to 
compare means of them with Posthoc test using R, following please see 
the output:

(CREB, mCREB and No virus are the name of samples)

 > nmda123
      Values      ind
1 6.7171265     CREB
2 5.0343117     CREB
3 6.9000000     CREB
4 0.1195394    mCREB
5 0.1221876    mCREB
6 0.1900000    mCREB
7 1.0000000 No Virus
8 1.0000000 No Virus
9 1.0000000 No Virus

 > nmda456
      Values      ind
1 6.4486940     CREB
2 6.2277490     CREB
3 6.5000000     CREB
4 0.2000000    mCREB
5 0.3766052    mCREB
6 0.4000000    mCREB
7 1.0000000 No Virus
8 1.0000000 No Virus
9 1.0000000 No Virus

 > TukeyHSD(aov(Values ~ ind, data = nmda456))
   Tukey multiple comparisons of means
     95% family-wise confidence level

Fit: aov(formula = Values ~ ind, data = nmda456)

$ind
                      diff        lwr        upr     p adj
mCREB-CREB     -6.0666126 -6.3289033 -5.8043219 0.0000000
No Virus-CREB  -5.3921477 -5.6544383 -5.1298570 0.0000000
No Virus-mCREB  0.6744649  0.4121743  0.9367556 0.0005382

 > TukeyHSD(aov(Values ~ ind, data = nmda123))
   Tukey multiple comparisons of means
     95% family-wise confidence level

Fit: aov(formula = Values ~ ind, data = nmda123)

$ind
                     diff        lwr       upr     p adj
mCREB-CREB     -6.073237 -7.5618886 -4.584585 0.0000392
No Virus-CREB  -5.217146 -6.7057976 -3.728495 0.0000943
No Virus-mCREB  0.856091 -0.6325606  2.344743 0.2588450

So my question is No virus-mCREB group. Even I looked at the data by 
eyes, there is big difference between no virus and mCREB in data 
nmda123, but why the pvalue is 0.2588450, but in nmda456 data, the 
pvalue is 0.0005382.  But I can see there is  bigger difference in 
nmda123 than nmda456, I do not know why. Sorry for my inexperiences in 
statistics.

Thanks for your reply and time!

Cheers,
Wei