Download PDF version

number of genes in the dataset.
7. Click Finish. The Experiment Progress dialog is displayed. It is dynamically
updated as the Median Scaling Normalization operation is performed. To cancel the
Median Scaling Normalization operation, click the Cancel button.
•
•
If the operation cannot complete an error message is displayed. The operation
will fail, for example, if the median of any sample is zero or near zero.
Upon successful completion, a new normalization dataset is added under the
original dataset in the Experiments navigator.
Related Topics:
Normalization Overview
Filtering Overview
Clustering Overview
Positive and Negative Control Genes
Overview
In some microarray experiments, there may be one or more control genes that can be
used to normalize between samples. With multiple controls, the median or mean is
calculated over all of the controls.
The control genes are always discarded prior to returning the normalized dataset.
Normalization Relative to Negative Controls
For each sample, this is done by subtracting the median or mean of the negative
controls within the sample. If you have only one control gene, the median or mean of the
negative control is the value itself.
For example:
Gene i sample j - median of the negative control genes within sample j
Gene i sample k - median of the negative control genes within sample k
Below is an example that illustrates the application with three control genes for each
sample:
GeneLinker Gold 3.1 / GeneLinker Platinum 2.1
268