This menu can be used to calculate the log-ratios from a two channel microarray. 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))
Transformation
| Log |
log-ratio = log(Red/Green)
|
Available Data
This lists data structures appropriate to the current input field. Double-click on a name to copy
it to the current input field; alternatively, you can type the name
directly into the input field.
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
Allows you to 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 |
Action Buttons
| Run | Run the analysis. |
| Cancel | Close the menu without further changes. |
| Options | Opens a dialog where additional options and settings can be
specified for the analysis. |
| Defaults | Set the menu settings back to the default settings.
Clicking the right mouse on this button produces a shortcut menu where you can choose to set
the menu using the currently stored defaults or the GenStat default settings. |
Example
This example shows the settings within the menu that can be used to calculate log-ratios from a GenePix file:
Additional options can be specified as follows:
See Also