R help - Jun 2012 - shapiro.test()

Hey,
today I wanted to use the shapiro.test() on data containing 3  
numerical values per group.
It is the first time that an NA was given back for some of the groups.
In the follwing an example of code and output is shown:

> shapiro.test(c(0.000637806, 0.00175561, 0.001196708))
	Shapiro-Wilk normality test

data:  c(0.000637806, 0.00175561, 0.001196708)
W = 1, p-value = NA

I am not able to find the bug in our data, so I think there might be a  
problem with the shapiro.test().

I use the following technical background:

platform       x86_64-pc-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          14.1
year           2011
month          12
day            22
svn rev        57956
language       R
version.string R version 2.14.1 (2011-12-22)


Thanks,
Judith

See

?shapiro.test

...the number of non-missing values must be between 3 and 5000.

By the way, how reasonable testing normality of 3 values?

Best
ozgur

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Actually, your sample size is 3. Sorry for that.

Ozgur

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On Jun 26, 2012, at 16:43 , reso at uni-potsdam.de wrote:
> Hey,
> today I wanted to use the shapiro.test() on data containing 3 numerical
values per group.
> It is the first time that an NA was given back for some of the groups.
> In the follwing an example of code and output is shown:
> 
> 
>> shapiro.test(c(0.000637806, 0.00175561, 0.001196708))
> 
> 	Shapiro-Wilk normality test
> 
> data:  c(0.000637806, 0.00175561, 0.001196708)
> W = 1, p-value = NA
> 
> I am not able to find the bug in our data, so I think there might be a
problem with the shapiro.test().
The clue is that
> diff(sort(c(0.000637806, 0.00175561, 0.001196708)))
[1] 0.000558902 0.000558902

which is either an extreme coincidence or a sign that your data are not
independent samples from a continuous distribution. Since the normal quantiles
are also equidistant, you get a correlation of W=1 in the QQ-plot, and
apparently this triggers the NA p-value.

I suppose returning p=1.0 would arguably be a better choice for this case, but
it _is_ pretty extreme.

-pd
> 
> I use the following technical background:
> 
> platform       x86_64-pc-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status
> major          2
> minor          14.1
> year           2011
> month          12
> day            22
> svn rev        57956
> language       R
> version.string R version 2.14.1 (2011-12-22)
> 
> 
> Thanks,
> Judith
> 
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
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Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com