Hi:

It strikes me as a little curious that the No Virus values in each of your
example data sets
are all *exactly* 1. Why is that?

Dennis

On Thu, Apr 29, 2010 at 4:52 AM, Yanwei Tan <Tan@nbio.uni-heidelberg.de>wrote:

> 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
>
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