[R] R Anova Analysis

Yanwei Tan Tan at nbio.uni-heidelberg.de
Thu Apr 29 13:52:12 CEST 2010

```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
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
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.