Plate View |
Thumbnail View |
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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.
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.
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.
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.
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. |
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.