Working With Tables

Tables are a particular kind of list, where the display has multiple columns for each item (row). The earlier section on Working with Lists covers everything that applies to both normal lists and tables, including selecting items (rows), adding and deleting items, moving items, etc. This section covers the additional details that apply only to tables, for example how to work with column sorting, etc. The section will also look at the general layout of the table that can be referred to when reading through the analyses sections further on in the manual.

Editing Tables

Samples

We will demonstrate editing table contents using the “MyGo Pro 10 fold Dilution Series.ppf” file from the MyGo Pro Demo Data folder, where we will edit sample data. Select Samples if not already selected.

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Editing Text in Tables

The names of samples can be added directly. To start editing, either double click the cell you wish to edit, or select it and then just start typing. You can now type and edit the contents as desired. Once finished, press Enter to edit the cell below, press Tab to edit the cell to the right or click outside the cell to finish editing.

Editing Predefined Text in Tables

Other cells have pre-defined contents that can be chosen by using a drop down menu. In the example below the Targets pane in Samples contain Dyes that can be chosen by using the drop down menu. Simply click the cell and the drop down menu will appear. Press Enter or click on the desired dye to make a selection.

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Editing Tick Selection Cells

Some Tables contain cells that have a tick box to enable or disable a feature. For example, in the example above the x174 target can become a reference by clicking the tick box as shown below:

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Furthermore, a cell can also be excluded from an analysis by clicking the Excl. box which is present in all analysis types under the Results as Table pane.

Editing Color in Tables

Some items, for example samples and targets, can be given different colors to distinguish them in table and graph displays. To edit a color, double-click the cell where they are displayed, to display the window shown below:

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Select the color you wish to use and click OK. The color you choose for samples and targets will now be used throughout the experiment in all analyses types using that sample and/or target.

General Table Layout

The table layout will be generally the same throughout the analyses types, however certain columns may not be in use or may be altered slightly depending on what analysis type you are looking at. The table that shows results for all analyses types is Results as Table.

Results as Table

The following diagram shows a table layout that most analyses types use for analysing results. It consists of rows and columns:

Rows

Each row of the table represents a well of the plate. These can be clicked or dragged as normal to select one or more wells. The selected wells’ data is also highlighted in the amplification graph, as normal. In the screenshot below, all wells are selected.

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Columns

Each column of the Results as Table displays different information for all wells. Below is a diagram describing the information present in each column:

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  1. Position in the plate.

  2. Index in the plate.

  3. An optional Note about the well itself. This can be edited by double clicking the cell.

  4. An Excl. column. This controls whether each well is included or excluded from the analysis. By default, all wells are included, and so all wells have an unticked entry in the exclusion column. By clicking on the checkbox in the Excl. column, a well can be excluded from all analysis. This is useful when a well is clearly an outlier, or if an error has occurred in pipetting or amplification. When excluding a well, you may also want to add a note to that well to indicate the reasons for exclusion.

  5. The name of the Sample present in the well, blank if no Sample is present.

  6. The name of the Target which describes the dye used for the experiment. In this experiment, we have only used one dye, so there is one set of columns giving data for this dye. In a two color experiment, there would be two sets of columns, etc. The following columns contain information for each Target present in the experiment.

  7. A Type, column showing an icon for the type of Target present - for example standard, negative, unknown. For standards, the quantity of the target is also shown.

  8. A Cq, showing the Cq value derived from the amplification curve by the Cq calling method.

  9. A “+” column, showing a tick for wells which had a positive amplification for the target, and no tick mark for wells which had no, insufficient or invalid amplification.

  10. A Quantity column showing the estimated quantity of the target present before amplification. Where standards are present and show positive amplification, they are used to build a standards curve to estimate quantity. Otherwise, quantity is estimated based on a fixed efficiency and offset - for more details see later section on Quantifiers.

  11. Data for each Results as Table can be exported by selecting the Export… button. For more information see Data Export.

Any additional columns in the Results as Table for a specific analysis type will be described in the corresponding manual section for that analysis.

Sorting Tables

Many table displays can be sorted. Note that in some tables, the order of the entries is important - for example in the list of stages in a cycling phase. In these cases, sorting is not possible. The Results as Table display of the example Absolute quantification experiment can be sorted:

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To sort the table by the values in a column, just click the header at the top of the column, where the name of the column is displayed.

Sorting by Type

Click the Type column of the Results as Table display. The column header will now display a small arrow pointing upwards, indicating the table is sorted by Type.

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Clicking the column header again will sort by decreasing Type value for a well, displaying a small arrow pointing down in the column header:

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It is also possible to sort by the values in multiple columns. Hold down the Ctrl key, and then click each column header that you want to sort by. Start from the least significant value, and proceed through to the most significant value (the primary sorting field). Each column can be clicked multiple times to toggle the sorting order until it is correct. When you are finished, release the Ctrl key.

We will sort so that we have samples grouped together, but with each set of replicates of a sample sorted by Cq. First, hold down the Ctrl key, and click the Sample column header. The table is now sorted by Sample.

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Now click the Cq column header, and release the Ctrl key:

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The data is now sorted so that we see the samples named “1e6” first, then the next sample name of “5e5”. Within each sample’s replicates, we have the lowest Cq value first.

To return to the normal order of data, just click on the # column header. This column displays the index of the row of the table (which is also the well index), and so sorting by this column returns us to the normal sorting order.

When data is exported (see Data Export), the data is exported using current sorting order.