Scaling in Data Manager
Open the Data manager by either pressing the Data manager button, or choosing Data Manager in the Tools menu, both found in the main window. The scaling of data is done under the Data selection tab in the Data manager which is open by default when the Data manager is opened. By default, there is no scaling. There are four different scaling options found in the drop-down list down to the right.
Make sure that you know what columns and rows represent when you scale your data, because scaling on columns or rows will produce different results. Usually, genes are arranged in columns and samples in rows, but if the data set have been transposed, it is the other way around. If the active data set is transposed, it is indicated in the status bar in the bottom of the main window, and you can also see it under the Row/Column tabs in the Data manager.
Scaling in the Data manager is reversible and does not affect the underlying data file(s) in the active data set. Scaling in the Data editor, on the other hand, is irreversible and changes the data permanently. A way of comparing the effects of different scaling, clone the data set and change the scaling of the clone. Analyze the two data sets separately and compare the results.