That's why I am suspecting actually the raw data. At the problem points there might be not included values or missing values where not exist on the normal plots.

I will find the original data and feed boxplot with it to see how it effects the final result.

Gökhan

On Wed, May 13, 2009 at 12:58 PM, Josh Hemann <jhemann@vni.com> wrote:

Thanks for sending the data and code. After playing around some I still don't

have a confident guess as to the problem (or solution), but here is what I

would look at more...

I issued plot(d[i][8:]) for i 0,1,...11 and looked at the shape of the

lines. For the two problem boxes, the plots of the associated data have

steep jumps between the 5th and 25th percentiles, when compared with the

data associated with the "good" boxes. So, what you have calculated as the

5th and 25th percentiles are not necessarily calculated by boxplot as such

because boxplot does not know that you are handing it percentiles of your

underlying data: boxplot actually computes the percentiles assuming that the

input _is_ the raw data. I would guess that if you gave boxplot the raw data

you would not see this issue of missing whiskers.

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