A biological circumstance? Interesting. Nothing immediately pops to mind.

cor 1-cor 1-abs(cor)
1 0 0
0.9 0.1 0.1
0.8 0.2 0.2
0.7 0.3 0.3
0.6 0.4 0.4
0.5 0.5 0.5
0.4 0.6 0.6
0.3 0.7 0.7
0.2 0.8 0.8
0.1 0.9 0.9
0 1 1
-0.1 1.1 0.9
-0.2 1.2 0.8
-0.3 1.3 0.7
-0.4 1.4 0.6
-0.5 1.5 0.5
-0.6 1.6 0.4
-0.7 1.7 0.3
-0.8 1.8 0.2
-0.9 1.9 0.1
-1 2 0

looking at the numbers; anything that is highly correlated ,whether
positively or negatively, will be close in distance. the heatmaps look
different and obviously the clustering is different.

Thanks. .

On Wed, May 11, 2011 at 9:19 PM, Kevin R. Coombes <kevin.r.coombes@gmail.com
> wrote:

> This is not really a bioconductor question.... but
>
> You need something that behaves like a "distance".
>
> By the definition of what you mean by 'distance", two things are close if
> and only if the distance is near zero.  The bigger (more positive) the
> distance, the further apart things are. And you cannot measure distances as
> negative; only non-negative values need apply.
>
> Using 1-cor, you are taking two things to be close if the correlation is
> close to 1.
> And the things that are furthest apart are the ones where the correlation
> is close to -1.
>
> As an exercise, you might want to think about circumstances where the
> preferred code would be
>    1 - abs(cor(*))
> instead of
>    1 - cor(*)
>
>
> On 5/11/2011 3:12 PM, john herbert wrote:
>
>> Dear bioconductors,
>> > From a google search, I found the following code that confuses me a
>> little.
>> As usual, it is probably something really elementary but reading around
>> does
>> not solve.
>>
>> The code was written by James Mcdonald (
>> http://www.mail-archive.com/r-help@r-project.org/msg61514.html) and is to
>> compute dendograms based on correlation and plot the results on a heatmap
>> as
>> follows;
>>
>> a<- matrix(rnorm(50), ncol=5)
>> rowv<- as.dendrogram(hclust(as.dist(1-cor(t(a)))))
>> colv<- as.dendrogram(hclust(as.dist(1-cor(a))))
>> heatmap.2(a, scale="row", Rowv=rowv, Colv=colv)
>>
>>
>> Why the *1*-cor(a)?
>>
>>
>> Orig.cor Adjusted cor
>> 1       0
>> 0.9     0.1
>> 0.8     0.2
>> 0.7     0.3
>> 0.6     0.4
>> 0.5     0.5
>> 0.4     0.6
>> 0.3     0.7
>> 0.2     0.8
>> 0.1     0.9
>> 0       1
>> -0.1    1.1
>> -0.2    1.2
>> -0.3    1.3
>> -0.4    1.4
>> -0.5    1.5
>> -0.6    1.6
>> -0.7    1.7
>> -0.8    1.8
>> -0.9    1.9
>> -1      2
>>
>>
>> This removes negative numbers? What is the reason for doing this?
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>

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