Hi Guys,

I need to cluster some samples A,B,C based on the gene expression (Please see the data below). I made a matrix of 1s and 0s where 1 indicate gene is present and zero indicates its absence. While I am clustering them using Hierarchical clustering (HC) method, samples A and C are clustered closely. But, as we can see, samples A and B share 2 genes in common. I understand how the HC algorithm is working. It is clustering based on both 1s and 0s. But, is there any other method we can apply to cluster samples A and B closely, (like avoiding zeros and clustering based on only 1s) ?

Sample    GeneA    GeneB    GeneC    GeneD    GeneE    GeneF    GeneG    GeneH    GeneI    GeneJ    GeneK    GeneL    GeneM    GeneN    GeneO    GeneP    GeneQ
A         0        0        0        0        0        0        0        0        0        0        0        0        0        0        1        1        0
B         1        1        1        1        1        1        1        1        1        1        1        1        1        1        1        1        1
C         0        0        0        0        0        0        0        0        0        0        0        0        0        0        0        0        0

Thanks in advance