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Generate Ratios (Two-Color Array)

The "Generate Ratios (Two-Color Array)" command will generate ratio data from a two-color array file. This module is most commonly used with two color Agilent or Genepix scanner data, when the user wants to import the individual colors first, before calculating the ratios. If the user has dye swap data, this module should be used before running the dye swap module, if choosing to import both colors and not a ratio.




  • The window includes a dropdown box to select the Project and Data object on which the command will be run.
  • Selections can be made on which variables should be included in the correlations (options include "all", "selected", "visible", and any pre-generated Lists).
  • Selections can also be made on which observations should be included in the correlations (options include "all", "selected", "visible", and any pre-generated Lists).

After importing two color data with separate channels, there will be two columns (ArrayID and Channel). Optionally, normalization can be performed before calculation of the ratios.


  • Array ID - Corresponds to the array that the data was imported from.
  • Channel - Channel will either be Channel1 or Channel2. The new dataset will calculate the ratios of channel2/channel1 and generate a new dataset.
  • Normalization Method - Both Lowess and Qspline normalizations are available for selection.
  • Perform log2 transformation - This will log transform the data if desired.
  • Ignore unmatched observations - Any unmatched observations can be ignored and ratios will not be generated. This would be for cases where both colors were not imported, or one color was eliminated by QC. If this is unchecked, the program will throw an error.