Parameter options
1. Output type:
Bait-bait comparisons can be output in two different types. Select the type here. By default,
images will be output as the "versus" plot type.
2. Primary filter value:
All preys that satisfy this cutoff for the control bait will be displayed in the scatter plot. For the
"fold-change" plot type, these preys will be displayed at the largest circle size, while in the
"versus" plot type, they will be shown in blue.
3. Secondary filter value:
All preys that satisfy this filter will also be displayed on the scatter plot. For the
"fold-change" plot type, these preys will be shown at a smaller size than those that passed the primary
filter, while in the "versus" plot type, they will be shown in
light blue.
4. Control subtraction:
The average value of a prey across control samples will be subtracted from the detected value for the bait
if this is set to "yes". The quantitative value for the prey becomes the value above and beyond what is seen
across the control samples. Specify the column to use for controls in the adjacent "Control column" field.
5. Normalization (none by default):
No normalization is applied by default, but when baits in the same dataset have been run on
instruments with varying sensitivity or dynamic range, normalization should be applied. The
options for normalization are to divide by the total abundance for all proteins identified
in the run or normalize based on a specific prey.
Normalization will be applied after control subtraction if both are specified.
6. Log transform (default no):
If desired, data can be log-transformed by base 2, base 10 or natural on the "versus" plot type.
Log transformation will be performed after control subtraction and/or normalization if these are also
specified.