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

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. tube experiments) no well IDs are defined and the plate view may be empty, but the samples can still be found in list view.

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

Well coloring

In the plate view, the sample wells are shown with sectors color coded according to the analysis results for each analyte in the well. The colors (red / orange / green) are determined by the number of probes meeting certain quality metrics. Two quality schemes are defined, which can be selected with the QC dropdown menu at upper right of the plate view. See sample quality for further detail.

The QC information about a sample portrayed in the graphic is also available in text form by hovering over the well.

Defining experiments

A key function of the plate view is to group wells into experiments.

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

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.

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 selecting them and clicking the Negative button.

Popup menu

Plate view has an extensive popup menu. The popup menu is the same between list and plate view. The following items are available.

Command	Function
Switch view	Alternate between list view, plate view, and undocked view
Dock / undock	Pop out an undocked view of the plate, or return to single frame. Especially useful for 384 well and 1536 well plates.
Samples > Select all wells	Select all the wells on a plate
Samples > Copy	Copy selected samples to a new plate
Samples > Move	Move selected samples to a new plate
Samples > Delete	Delete samples from plate
Apply sample sheet	Reads a sample sheet and uses it to rename and/or group samples. The file may be either CSV or XLSX.
Export sample sheet (list form)	Generate a sample sheet template, as a list in CSV format.
Export sample sheet (table form)	Generate a sample sheet template, as a table in XLSX format.
Dilution series	Use a selected set of wells to define a dilution series. The selection is normally rectangular. The long axis of the rectangle is taken as the dilution direction. The short axis of the rectangle is taken as deplicates. For instance a rectangle of 8 rows and 3 columns is interpreted as 8 serial dilutions replicated 3 times. The well furthest to the left and top is taken as dilution 1.0, then each well along the dilution direction is divided by the dilution factor relative to the previous one. If the selection has two long columns and two short columns, the first long column and first short column are treated as a single dilution series, and the second long and second short column are similarly combined. For more complex dilution series (e.g. irregular dilutions, skipped rows, etc) it is recommended to use a sample sheet.
Clear all dilution series	Erase the current dilution values assigned to samples on this plate
Define variables	Pops up a visual editor to define variables
FCS>Show FCS Parameters	Pops up a frame with the FCS settings for this well, e.g. gain, instrument, timestep, etc.
FCS>Save FCS parameters to file	Saves FCS settings of this well to CSV
FCS>Pool selected samples	Pools the events of the selected wells and replaces the pooled wells with a single well containing all the events
FCS>Pool samples by replicate	Automatically pools wells which share the same replicate name. An experiment must be defined and a variable "Replicate" must exist.

Creating a new (sub) plate

When a set of samples is selected and either copied or moved, a new sub plate is created with just the wells that were highlighted. It should automatically pop to the front, if not, use the thumbnails to find it. Creating sub-plates is essential when several different kits are run on the same plate, where the different kits have incompatible code maps. Treating them together on one plate will lead to incorrect analysis.