scale in R pheatmap

Question

[acfasantos]

Hi, I am having trouble understanding the scale() function in R. Anyone could explain it to me? Because my clusters change with scale option.

[acfasantos]

The option that i am using os scale="column" . This tranform my values?

[Prakash]

yes, of course. you may try it row for clustering row-wise.

[Kevin Blighe]

In addition, take a look here: A: cannot replicate the pheatmap scale function

Answer 1

[Prakash]

scale function is used to transform the values. values are scaled using mean and standard deviation (link). While clustering, scaling is generally performed to obtain better cluster. clustering would change based on other parameters also such as distance method.