J-Express Pro provides a number of methods of modifying a data set. The modified data set will be available in the J-Express project tree as a separate node under the node it was created from.
Always log(2) transform intensity values and ratios. Why? Because Terry Speed says so: http://www.stat.berkeley.edu/users/terry/zarray/Html/log.html
1. Select the data set you want to transform from the J-Express project tree.
2. Click the 
( Create Sub Data Set ) button from the J-Express Pro tool bar, or select Data Set | Create Sub Data
Set from the J-Express Pro menu bar. The Create data set window will open.
3. Select Log(2) Transform All Data
4. Click Ok.
Mean normalisation means that all the values in an expression profile are changed by the same amount so that the mean expression value becomes 0, i.e. the mean expression value is either subtracted from all data points or added to all data points. This makes it easier to visualise up and down regulated genes, as well as visually identify different genes that follow similar trends.
1. Select the data set you want to transform from the J-Express project tree.
2. Click the ( Create Sub Data Set
) button from the J-Express Pro tool bar, or select Data Set | Create Sub Data
Set from the J-Express Pro menu bar. The Create data set window will open.
3. Select High Level Mean Normalization
4. Click Ok
Scale normalisation will scale the array intensity values against the other array intensity values to make the distributions more similar, hence comparable. See
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP.
Department of Statistics, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720-3860, USA.
Nucleic Acids Res. 2002 Feb 15;30(4):e15.
1. Select the data set you want to transform from the J-Express project tree.
2. Click the ( Create Sub Data Set
) button from the J-Express Pro tool bar, or select Data Set | Create Sub Data
Set from the J-Express Pro menu bar. The Create data set window will open.
3. Select Scale Normalization
4. Click Ok