scale in R pheatmap
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3.2 years ago
acfasantos • 0

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

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

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

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

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3.2 years ago
Prakash ★ 2.2k

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.

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