[R] calculate Euclidean distances between populations in R with this data structure

[Sarah Goslee]

I'd probably start with ?dist

Sarah

On Thu, Sep 4, 2014 at 4:10 PM, Ding, Yuan Chun <ycding at coh.org> wrote:
>
>
>
> I want to calculate Euclidean distance between 12 populations, in each population there are 20 samples and each sample is measured for 100 genes (these are microarray data; the numbers here are just examples).
> The equation I found is:
> distance = sqrt{[sum(Average of xi -average of yi)^2] /n }, i=1 to n;
> where xi and yi are the expression of gene i over two populations with p and q samples (x1, x2,...,xp), (y1, y2,...,yq), n is the number of genes.
> part of data are pasted below
> row.names pop1.1    pop1.2  pop1.3  pop1.4  pop2.1  pop2.2  pop2.3  pop2.4
> 7A5     5.38194 4.06191 4.88044 5.60383 6.23101 6.53738 4.80336 5.86136
> A1BG    5.15155 4.29441 4.59131 4.90026 4.62908 4.48712 4.73039 4.46208
> A1CF    4.22396 4.14451 4.41465 3.93179 4.89638 4.66109 4.20918 4.48107
> A26C3   12.1969 12.4179 10.9786 11.7659 11.405  11.7594 11.1757 11.8128
> How might one calculate these distances in R with this data structure?
>
>
> Thanks,
>
> Ding
>

-- 
Sarah Goslee
http://www.functionaldiversity.org