Plate View

The plate panel provides a detailed view of a single plate, as well as a navigation aid to other plates that have been loaded.   Clicking on different plates in thumbnail view will bring focus to the selected plate. 
Plate View
Thumbnail View
regular plate view
plate thumb view

The plate in focus can be viewed in plate view (default) or in list view.     To toggle between one view and the other, use the popup menu (right-click).   If the samples do not come from a plate (e.g. single well experiments) no well IDs are defined and the plate view may be empty, but the samples can still be found in list view.    The popup menu is the same between list and plate view, and provides access to several functions.

The list view is shown below.   The samples are given default short names according to their well position, if read from a plate.  The full names of the sample are derived from the file from which they originated.   The quality score depends on the data source and measures the quality of data in that sample.
List View

In the plate view, the sample wells are shown with sectors color coded according to the analysis results for that well.   The colors (white/orange/green) are determined by the number of probes whose signals are found to have a good confidence interval (green = good: CI is < 15% of mean signal; orange = fair: CI is between 15% and 25% of mean signal; white = poor: CI is > 25% of mean signal). Thus a mostly green well indicates that the results (a high or a low signal indicating a high or low concentration of the target) are reliable for that well.   In a picture:

The advanced view uses the same sector-coloring, but if the data is directly from an FCS file, the well is filled to a size proportional to the number of particles successfully recognized and assigned to a probe as a fraction of the number expected under ideal conditions. Thus a well may be colored mostly green, with only a few probes for the white or orange sectors, but may be displayed with a very small area because while the proportions of the results are as indicated, they are based on a smaller total number of particles.

In the same session where raw data (FCS, sequence data) has been loaded, all the information about a sample portrayed in the graphic is also available as text by hovering over the well.

Defining experiments

A key function of the plate view is to group wells into experiments.   In most assays, samples will appear as groups.   For instance, all the wells in a single row may contain the same sample, the bottom row may contain controls, and so on.    

To define a group, select a rectangle of wells.   Then right click it and select the Experimentbutton.   The experiment will appear on the Experiment Panel.     Experiments are given an automatic name, which can be changed.

Experiments can overlap.   It is often useful to have an "All" experiment in addition to the individual experimental groups, for a first tour of the data.  

Individual wells can be Experiments.   

An irregular block of sample wells can also be defined as an experiment, by ctrl-clicking a series of wells prior to defining an experiment.

Creating a new (sub) plate

A subset of samples may be defined as a new plate.   Select samples as usual, right-click, and choose "Create New Plate".  A new plate  is created with just the wells that were highlighted.  (If should automatically pop to the front, if not, use the thumbnails to find it).  The original plate is unchanged.    Creating sub-plates is particularly desirable in cases where several different kits were run on the same plate, where the different kits might have incompatible code sets.   Treating them together on one plate will lead to incorrect analysis.

Deleting a plate

In thumbnail view, point at the plate to delete and use the right-click popup menu.  Deleting a plate does not delete the experiments defined using samples from that plate.

Defining negative controls

Samples can be defined as negatives by selectingthem and clicking the Negative button.

Other popup menu items

Command Function
Rename Samples
Use a sample sheet to rename samples and add groups.
Delete samples Removes samples from the plate.  Also removes them from all experiments that have samples from that plate.
Clear all dilution series
Clears the dilution values for all samples on this plate
Assign to replicate
The selected samples are assigned a replication group.   
Pool samples by replicate Combines multiple FCS samples into a single "super-sample" with all the particles of the samples in the super-sample.    Samples are pooled if they have the same value of the variable called "Replicate".
Copy samples to new plate
A new plate is created with just the selected samples.   This is most useful if a plate contains samples with multiple different PLXs.   Each PLX must be analyzed on a plate of its own.
Show FCS parameters
Displays the parameters of the FCS run, such as gain settings, instrument used, etc.
Toggle list view
Toggle between plate view and list view

See Also

Plates, Experiments, Datasets

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