[BioC] How to do clustering

[Sean Davis]

ssls sddd wrote:
> Dear Dr.Thomas Girke,
> 
> I have one more question for you. I tried pvclust in the session of
> 'Obtain significant clusters by pvclust bootstrap analysis' for my data, x.
> 
> But I have a problem with:
> 
> heatmap(x, Rowv=dend_colored, Colv=as.dendrogram(hc), col=my.colorFct(),
> scale="row", RowSideColors=mycolhc)
> 
> the error was:
> 
> error in heatmap(x, Rowv = dend_colored, Colv = as.dendrogram(hc), col =
> my.colorFct(),  :
>         'x' must be a numeric matrix
> 
> I ran 'x[1:3,1:3]' and it produced the following:
> 
>               AIRNS_A09 AIRNS_A11 AIRNS_A12
> SNP_A-1780271   1.85642   1.50956   1.73154
> SNP_A-1780274   1.72140   1.83712   1.85948
> SNP_A-1780277   2.04241   1.53458   1.65270
> 
> I think the x is a numeric matrix. Do you think where I may get wrong?

Try coercing the x into a matrix directly:

heatmap(as.matrix(x), Rowv=dend_colored, Colv=as.dendrogram(hc),
col=my.colorFct(), scale="row", RowSideColors=mycolhc)

Does this fix the problem?  You can always check the class of an object
by doing something like:

class(x)

which should report:

[1] "matrix"

Hope that helps.

Sean