Calculate Microarray Log-ratios

Select menu: Stats | Microarrays | Calculate | Log-ratios

Use this to calculate the log-ratios from a two channel microarray.

After you have imported your data, from the menu select
Stats | Microarrays | Calculate | Log-ratios.
Fill in the fields as required then click Run.

You can set additional Options before running the analysis by clicking Options.

There are options for background correction and setting the channels to a minimum value to avoid large variation when the values in either channels get close to zero. The ratios are logged as the variation usually increases with the size of the mean. However, although the variation may be more uniform with the logged ratios, it may still show considerable heterogeneity with different levels of intensity.

The intensity of a spot is defined as:

Intensity = (LOG(Red) + Log(Green))/(2*LOG(2))

Available data

This lists data structures appropriate to the current input field. Double-click a name to copy it to the current input field or type the name.

Transformation

Log

log-ratio = log(Red/Green)

Red foreground

The variate containing the values of the red/Cy5 foreground for each spot. Note: Cy5 is the technical name for the red fluorescent dye.

Green foreground

The variate containing the values of the green/Cy3 foreground for each spot. Note: Cy3 is the technical name for the green fluorescent dye.

Background correct red and green values

When selected, the level of the background (specified in the fields provided) will be subtracted from the foreground levels before taking the log-ratios.

Red background

The variate containing the values of the red/Cy5 background around each spot. This is only required if background correction is to be performed.

Green background

The variate containing the values of the green/Cy3 background around each spot. This is only required if background correction is to be performed.

Smooth background values

When selected, this performs a two dimensional smooth of the background values and uses the smoothed values for the correction, rather than just using the individual background for each spot which may be more variable than a smoothed value. Note that this can be time consuming for large slides. If this is selected the Rows and Columns must be provided.

Rows

A factor indexing the rows over the whole slide. Note that care must be taken not to provide a factor that only indexes the rows within a pin.

Columns

A factor indexing the columns over the whole slide. Note that care must be taken not to provide a factor that only indexes the columns within a pin.

Save

Lets you specify names to store the results.

Log-ratio	Variate	The calculated log-ratio or generalized log-ratio transformation of the red and green values for each spot
Intensity	Variate	The intensity of each spot

Display in spreadsheet

Select this to display the results in a spreadsheet.

Action buttons

Run	Run the analysis.
Cancel	Close the dialog without further changes.
Options	Opens a dialog where additional options and settings can be specified for the analysis.
Defaults	Reset the options to their default settings. Clicking the right mouse on this button produces a shortcut menu where you can choose to set the options using the currently stored defaults or the Genstat default settings.

Action Icons

	Pin	Controls whether to keep the dialog open when you click Run. When the pin is down the dialog will remain open, otherwise when the pin is up the dialog will close.
	Restore	Restore names into edit fields and default settings.
	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.