Parameter Profile Descriptions

The Parameter Profiles available in GemStone provide great flexibility for modeling different intensity characteristics for parameters in the progression being modeled.

The general rule for choosing a profile is to choose the simplest one that describes the intensity changes you expect to find in your samples. Start with a simple profile, and then as the model becomes well-defined and additional structure appears, a more appropriate profile can be selected.

Constant

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This profile has 2 Control Points that are linked to the same intensity. It is most often used to select events for a subset.

Increasing

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This profile has 2 Control Points. The first point is forced to have a lower intensity than the second. It can be used on Time parameters to order events based on acquisition time.

Decreasing

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This profile has 2 Control Points. The first point is forced to have a higher intensity than the second.

Step Up

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The Step Up profile has 4 Control Points. The first 2 points are linked to have the same intensity values. The last 2 points are also linked, and are forced to have a higher intensity than the first two. It is used for parameters that are up-regulated in the progression being modeled.

Step Down

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The Step Up profile has 4 Control Points. The first 2 points are linked to have the same intensity values. The last 2 points are also linked, and are forced to have a lower intensity than the first two. It is used for parameters that are down-regulated in the progression being modeled.

Three, Four, Five Levels

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These profiles are very flexible, used to define 3, 4, or 5 levels of intensity. For each level, there are 2 Control Points that are linked to the same intensity for the parameter. Each of the levels has no dependencies on the other levels. In other words, the next level can be higher, lower, or even the same intensity as its neighboring level.

Cell Tracking 5, 6, 7, 8

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These profiles are used for modeling cells stained with cell-tracking dyes, like CFSE and PKH-26. With these dyes, there is a well-defined relationship of intensity from one level to the next. When the cells divide, each daughter cell takes half of the cell-tracking dye. Therefore, the intensity drops by 50% from one generation to the next.

When choosing between profiles for 5, 6, 7, and 8 generations, choose the one that will accommodate the divisions in the full course of the experiment.

Increase and Level out

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This profile has 3 Control Points. The first point is forced to have a lower intensity than the others. The second and third points are forced to have the same intensity values. It is used for parameters that up-regulate at the beginning of the progression, and then level off.

Decrease and Level out

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This profile has 3 Control Points. The first point is forced to have a higher intensity than the others. The second and third points are forced to have the same intensity values. It is used for parameters that down-regulate at the beginning of the progression, and then level off.

Up Pulse

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This profile has 5 Control Points that are used to model an up- and down-regulation in the progression. The first 2 points are forced to be on the same intensity level. The third point is forced to be higher than the others. The last two points are locked to the same intensity level, but the level can be different than the first level.

Down Pulse

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This profile has 5 Control Points that are used to model a down- and up-regulation in the progression. The first 2 points are forced to be on the same intensity level. The third point is forced to be lower than the others. The last two points are locked to the same intensity level, but the level can be different than the first level.

Constant Increase Two-fold Constant (DNA)

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This profile is similar to the Step Up profile, but is specifically designed to be used with linear parameters that have a 2-fold increase in the progression. It is most commonly used for DNA parameters, where the G2-M intensity is twice that of the G0-G1 intensity.

Up Constant Down

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This profile uses 4 Control Points to model an up-regulation, leveling off, and ending with a down-regulation.

Custom 2 through 10 Point

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These profiles are extremely flexible. There are no linkages or dependencies on the points, so the shapes they can model are very open ended. In most cases, it is best to choose a simpler, more constrained Parameter Profile instead of a Custom profile. In general, simpler profiles create more robust models.