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Hi Thomas,<br>
Thanks for your answer I will start to play around and I will let
you know.<br>
<br>
Best<br>
Jose<br>
PS:BTW, I just wanted to confirm that the bug is as you said.
Changing the name of the object my.data solves the problem.<br>
<br>
<br>
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On 11/25/2010 06:05 AM, Thomas Friedrichsmeier wrote:
<blockquote
cite="mid:201011251205.47169.thomas.friedrichsmeier@ruhr-uni-bochum.de"
type="cite">
<pre wrap="">Hi,
welcome to the list, and thanks for your offer to help. Let's see if we can get
you going:
On Thursday 25 November 2010, Jose Maria Polo wrote:
</pre>
<blockquote type="cite">
<pre wrap="">The first one that I would like to propose is hierarchical clustering (HC).
A simple HC, basically a front end for hclust (transposing the data (d)
and generating a distance matrix (dist) will be necessary first).
> t.r = t(data)
> dist.tr = dist(t.r)
> hc.tr = hclust(dist.tr, method = "average")
> plot(hc.tr, hang = -1)
Another approach could be to call pvclust, which it calculates something
similar. However it also gives p values.
> result <- pvclust(data, method.dist="cor", method.hclust="average",
nboot=1000)
> plot(result)
What do you think?
</pre>
</blockquote>
<pre wrap="">
Frankly, I have no idea which of these approaches is better. Unless pvclust
(which package is that?) offers significant advantages compared to the approach
usin hclust, I'd lean towards using hclust. Since that is in the official
"stats" package, this will allow to use the plugin without installing an add-
on package. Also it's a very safe bet that the functions in the "stats"
package will continue to be supported and stable in the long term.
</pre>
<blockquote type="cite">
<pre wrap="">Anyway, I am not writting to just make a suggestion. I would like to
help as much as I can with this, even if I never have program anything.
</pre>
</blockquote>
<pre wrap="">
Great!
</pre>
<blockquote type="cite">
<pre wrap="">I already started reading the information about how to generate a plugin.
As suggested in your plugin webpage, I guess that the best way will be
to start modifying a plugin that has a similar role.
Ideally should be a pluggin that allows to compare as many variables as
we want (I was thinking to use the boxplot plugin, but I realized that
the boxplot plugin use many variables, but all separated).
Any idea or suggestions?
</pre>
</blockquote>
<pre wrap="">
Well, the boxplot plugin may not be the easiest one to start with, as it's a
comparatively complex one. Perhaps barplot or dotchart are easier to handle
for the start.
In order to support multiple variables, you probably want to generate R code
like this, as a very first step:
data <- data.frame (var_a, var_b, var_c, ...)
This is to collect all selected variables into a single data.frame.
Achieving this is not all that hard. First make sure, the <varslot> in your
.xml-file has the attribute multi="true", to allow selection of serveral
variables. Then, in the .js-file, use:
var xvarsstring = getValue ("x").split ("\n").join (", ");
echo ('data <- data.frame (' + xvarstring + ')\n');
</pre>
<blockquote type="cite">
<pre wrap="">2) I am not sure if I should report this here, but I think that I found
a bug, when I try to use basic statistic the "submit" botton does not
turn on.
</pre>
</blockquote>
<pre wrap="">
Thanks. This has been reported before, but I could never reproduce this. Now I
found out it happens when you have an object called "my.data" in the
workspace. Fixed in our SVN repository.
Regards
Thomas
</pre>
<pre wrap="">
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Jose Maria Polo, Ph.D.
Massachusetts General Hospital Center for Regenerative Medicine
Harvard Stem Cell Institute
185 Cambridge Street CPZN 4200
Boston MA 02114
617-643-5941 (tel)
617-643-3170 (fax)
<a class="moz-txt-link-abbreviated" href="mailto:polo.josemaria@mgh.harvard.edu">polo.josemaria@mgh.harvard.edu</a>
<a class="moz-txt-link-abbreviated" href="mailto:josemariapolo@gmail.com">josemariapolo@gmail.com</a> </pre>
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