Many microarray experiments are carried out on paired samples, a treatment sample and a control sample, and the resulting expression levels measured on the same chip with two different fluorescent dyes. The most common fluorescent dyes used are Cy3 (green) and Cy5 (red), so these experiments are referred to as two-color experiments, Cy3/Cy5 experiments, or red/green experiments.
GeneLinkerô can carry out certain operations when it has both the treatment and control measurements, operations it cannot carry out if it has only the ratios. In GeneLinkerô, we refer to a dataset which has both treatment and control values stored as Two-Color Data. In the description pane for such a dataset it will say Two Channels Available: Yes. If the description pane does not say this, then GeneLinkerô does not have the required two values for each spot and cannot treat the data as Two-Color Data. If you believe you imported two-color data but the description pane says Two Channels Available: No, re-examine your data and your choice of a data import template. Two-Color Data can be imported using GenePix, Quantarray and Scanarray templates, but not all templates of those types import two-color data. Please see the appropriate Formats and Templates pages for more information.
Certain operations are possible on Two-Color Data which are not applicable to regular data. These operations include Lowess Normalization and the Intensity-Bias Plot.
When you make a table view, color matrix plot, or other visualization of a table with two channels available, the data displayed are the ratios.
Selecting a Template for Data Import
Importing Data from GenePix Files
Importing Data from Quantarray Files
Importing Data from Scanarray Files