[BioC] How to calculate Pearson coefficient between 2 genes in a group including 1500 genes?

[Antoine Lucas]

On Tue, 01 Mar 2005 18:52:09 +0800
xpzhang <xpzhang at genetics.ac.cn> wrote:

> Hello,
> 
> I encountered a big difficult question now. I have a gene expression
> prifile, which incoulded 1500 gene and 20 treatment. I wanted to
> calculate the Pearson coefficient between any gene-pairs in the 1500
> gene. 

I think function Dist from package amap does this matrix
library(amap)
Dist(data,method="pearson")

or 
Dist(t(data),method="pearson")


 
> Firstly, I tried to use SAS 6.12 to do it. But I found that SAS can not
> read the all data, and it can only read 15 rows data. 

Well, this surprise me ! are you sure that data are not corrupted ?


Regards.

Antoine Lucas.

-- 
Antoine Lucas
Centre de génétique Moléculaire, CNRS
91198 Gif sur Yvette Cedex
Tel: (33)1 69 82 38 89
Fax: (33)1 69 82 38 77