**200**wrote:

I've seen the term been used in some papers working with gene expression data. I assume they refer to performing z-score normalization on the expression matrix, but I would like to know if this is the right interpretation. Also, is this typically done over each gene vector (rows of a traditional expression matrix) or over the samples? (columns). Another question I have is if it is always done one way or if it depends on the downstream analysis that we want to perform. For example, I've been encountering the term in co-expression papers, sometimes they also refer to this as "zero centering the expression matrix". What about if you want to do PCA, I think in R the function `prcomp`

by default performs the normalization on the columns, but could you in some situations do it over the rows before PCA?

**60k**• written 13 days ago by mike-zx •

**200**