| Calculate Microarray Log-ratios Options |
| See Also |
This dialog controls additional options and settings for the
Calculate Microarray Log-ratios
menu.
Background Correction - Degrees of Freedom for smooth
This option is enabled if the Smooth Background values option has been set on the main
menu. This specifies the degrees of freedom used in the function that smooths the background
red and green values. A small value for the degrees of freedom will create a smoother
but less responsive surface for each colour. A large value will create a rougher, more
variable surface that is able to respond to short term trends.
Set a Minimum value on both channels
This option is used to retain information on spots where the foreground is below
the background value on one colour. If this option is not set, then if one colour's
foreground is below the background, the log-ratio will be made missing despite the
value of the other channel, thus potentially missing a probe with a high level of
differential expression. Some image analysis packages set a very large constant
log-ratio for this, but this can bias the results as no differentiation
is made between cases where the other colour is just above background, and
other where the other colour is significantly above background.
This option can also be used to reduce variability at the low end of the intensity range,
as often the ratios become unstable as the foreground gets close to the background level.
Minimum Value
This is the value that will be used as a minimum value for both channels/colours.
If the Use Multiplier with Background Std Deviations option is selected, this value
will be multiplied by the background standard deviations.
Use Multiplier with Background Std Deviations
When selected, the background standard deviation for each colour is multiplied by the Minimum Value, so that the
minimum depends on the quality of the background around each spot.
Red Background SD
The variate containing the standard deviation of red background around each spot.
Green Background SD
The variate containing the standard deviation of green background around each spot.
Single Minimum per Slide
The minimum values per spot depending on the background standard deviations are
averaged over the whole slide and this single value is used for each channel.
This lets each slide have its own minimum, depending on how clean the background
values are. Slides with highly variable backgrounds will have larger minimum
values applied.
Add a constant to both channels
This option can also be used to reduce variability at the low end of the intensity range,
as often the ratios become unstable as the foreground gets close to the background level.
Adding a constant to both red and green will stabilise the log-ratios at low intensities,
but with a potential loss of sensitivity for detecting differential expression.
The constant is specified in the Constant edit field, and this
would normally be a positive value, although a negative value could be used if it where
thought the image analysis package was underestimating the background values.
Display Summary of Transformation
Display the 10th, 25th, 50th, 75th
and 90th percentiles of the log-ratios for each slide within the Output window.
Action Buttons
| OK | Store the options and close the dialog. |
| Cancel | Close the dialog without making any changes. |
| Defaults | Reset the options to their default settings. |
See Also