I'm using pvclust package in R to cluster (hierarchical clustering with bootstrap) my gene expression data. When I plot my data after clustering, all the branches collapse at the bottom and I can't see the clusters. Is there a way I can improve the image? I used the function scale to scale my data before clustering it but the tree that it produces is a little different from what is produced with unscaled data. With unscaled data, I get 3 outliers but with scaled data the outliers are embedded in the clusters. I'm worried that scaling is distorting my data. Please help.
Image with unscaled data:
If I scale the data:
I get this tree:
Gene condition1 condition2 condition3 AATF 0.004239637 0.004565341 0.004992545 ADNP2 0.00316361 0.002401833 0.002222395 AP-2 0.029882702 0.016730296 0.020585824 AXIN2 0.001743115 0.002124558 0.003573409