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Normalize Two Channel Microarray Date Store

Use this to save results from normalizing two channel microarray data. These results are saved when an analysis is run and must be specified before running an analysis.

  1. After selecting the appropriate boxes, type names for the data structures into the corresponding In fields.

Save

The table below indicates the type of structures formed for each item.

Corrected log-ratio Variate The log-ratios corrected for the fitted terms/effects.
Standardized log-ratios Variate The standardized corrected log-ratios = corrected log-ratios/smoothed standard deviations.
LR smoothed standard deviation Variate The smoothed standard deviations of the corrected log-ratios.
Corrected log (base 2) red values Variate The log2 red corrected for the fitted terms/effects. This is given by:
CALC cLogRed = Intensity + cLogRatio/2
Corrected log (base 2) green values Variate The log2 green corrected for the fitted terms/effects. This is given by:
CALC cLogGreen = Intensity – cLogRatio/2
Pin effects Table The fitted pin effects as a table indexed by slide and pin.
Row effects Table The fitted row effects as a table indexed by slide and row.
Column effects Table The fitted column effects as a table indexed by slide and column.
Intensity effects Variate The fitted intensity effects for each spot.

Display in spreadsheet

When selected, the saved results will be displayed in spreadsheets. The saved table results will also be displayed within new spreadsheet windows, and the variate results will be added to the originating spreadsheet for the log-ratios, if it is currently open in Genstat, otherwise to a new spreadsheet.

Action Icons

Clear Clear all fields and list boxes.
Help Open the Help topic for this dialog.

See also

 

Updated on April 29, 2019

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