[BioC] heatmap and hclust results

[kfbargad@ehu.es]

Dear list,

I obtained a dendrogram for a set of d.e genes using hclust() with 
the following code:

mygenes.tree<-exprs(mygenes.eset)
r = cor(mygenes.tree, method=”pearson”)
d = 1 - r
hc = hclust(as.dist(r), method=”average”)
plot(hc, labels = sampleNames)

and tried to compare it with a heatmap with the same genes:

heatmap(mygenes.tree, col=rbg, distfun = function(c){1 - Dist(c,method 
= "pearson")},hclustfun= function (d) {hclust(d, method=”average”) }, 
labCol= sampleNames,Colv=cov(mygenes.tree),Rowv=cov(mygenes.tree)))

but the grouping of the samples on both dendrograms is different. Is 
it because I am using some parameters that differ between both methods?
I have read the ?heatmap info and am not very sure that I understand 
the difference between the arguments Colv and hclustfun and whether 
they can be used together. Maybe I am introducing some confronting 
arguments without noticing. 

Could anyone check my code and help me on this?

I am using R 2.2.0

Thanks in advance,

David