I have data that refer to the number of occurrences of specific variable in samples:
V1 V2 V3 ... sample1 0 2 1 sample2 7 1 0 sample3 1 4 1 ....
The data refers to the occurrence of genes(V1...) in different genomes (sample1..).
I want to perform a cluster analysis combined with an heat map.
I used the function
heatmap.2 in the
gplot package in R.
I used Euclidian distances for calculating the distance among the samples.
The clustering algorithm is the default one for the function
hclust in R (
hclust(d, method = "complete", members = NULL)).
However, I am not completely sure it is the right method.
Any suggestion on how to choose the right method to calculate the distances among my samples?
EDIT The aim is to describe the distribution of the variables (genes) among the samples (genome), and cluster the samples(genomes) according with the values that each variables assume (meaning, how many specific genes are present)