Thanks Sean! It works well.

Sincerely,

Alex

On 6/11/07, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> ssls sddd wrote:
> > Dear Dr.Thomas Girke,
> >
> > Thank you very much for the info.
> >
> > I tried mydist <- as.dist(1-cor(t(y), method="pearson")) on my data but
> > it failed. My 'y' consists of 238000 observations (rows)  and 49 samples
> > (columns) and R said:
> >
> > error in cor(t(x), method = "pearson") : allocMatrix: too many elements
> >
> > Do you think I can make this work out in another way?
>
> For folks relatively new to R and Bioconductor, it is worthwhile the
> help pages for ALL new commands used.  In this case, the help page for
> cor() states that it will compute the correlation between all COLUMNS of
> the matrix, if given a matrix.  You have a matrix with 49 columns and
> 238,000 rows.  If you were to run cor() on that matrix, it would produce
> a matrix of size 49x49 containing all pairwise correlations between
> samples.  However, in this case, a transpose is applied first, so R is
> going to try to compute a 238,000x238,000 matrix of correlation
> coefficients.  I'm assuming that is not what you want and that you
> really want to cluster the samples.  Drop the t() and all will be well.
>
> Sean
>

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