It means transforming data to the Z-score aka standard score.
The Z-score indicates how much a value deviates from the mean across all values and by this is a relative measure of e.g. gene expression, fold changes, whatever you put in.
scale function can do that for you, e.g.
matrix is the expression matrix with columns = samples and rows = genes. Data should be appropriately normalized, e.g.
log2(normalized counts) with
normalized counts e.g. coming from the
edgeR normalization or from transformations such as
rlog (the latter two already on log scale so no need to log them again).