8/25/2023 0 Comments Apply compensation matrix flowjo![]() It is recommended to leave this value at zero unless these digitization errors become apparent. This will add a small random value to the linear value prior to it being reconverted back to log. Typically, this value should be less than one. However, if you notice digitization errors, you can enter a value to spread the grouped population out using the Range of random value to add when converting log data field (Figure 9.11). The conversion to linear and reconversion back to log occurs automatically during the software compensation process. Continue until the data is properly compensated. Repeat steps 8 through 11 using smaller and smaller increments as you refine the matrix. ![]() Press Preview, and IDEAS will apply the new compensation values to the training set. ![]() Depending on the resolution of your original file, this can result in digitization errors, which can cause large numbers of events to group in a single channel. A compensation matrix is calculated using single color fluorescent control files that are collected. It is then converted back to log for display. If you have stored data on a logarithmic scale in your FCS file (common with FCS 2.0 data files), this data has to be converted to a linear scale before compensation is applied. You may find it helpful to enter the date or experiment number as the compensation name.Ĭompensation must be performed on linear data. The name of your compensation may be changed at any time by selecting the compensation and clicking the Rename selected compensation button or by right-clicking on a compensation and choosing Rename. When a compensation value is manually adjusted, the compensation icon (red box at the top) becomes red highlighted, while the text value (red box at the bottom) becomes bold and underlined.Įvery compensation must be given a unique name. The matrix will be applied to the group assuming all parameters are the same.Figure 9.9. This matrix file can also be dragged to the group. Notice the sample A1 above now has a different color badge from the matrix we dragged on it. xml matrix file from your file system onto a sample in FJ to compensate that sample: You can apply a matrix stored on your file system to samples in your workspace assuming they have all the parameters listed in the matrix itself. The names must match exactly best practice is to use the names that appear in the $PnN keywords of the FCS file. Parameters/channels that are not in this list have not been compensated parameters/channels in this list that are not in the sample are ignored. The file contains the title of the compensation matrix, the names of the parameters/channels used in the matrix and the coefficients of the compensated parameters. The saved matrix file is written in standard XML and is based on standards developed by the Data Standards Task Force (DSTF) of the International Society for the Advancement of Cytometry (ISAC). FlowJo uses XML to express these matrices.Įxample matrix file, viewed in Mozilla Firefox browser. Once in the Matrix Editor, you can use the File -> Save Matrix command to export it. The matrix editor is easily accessed by double-clicking a sample’s compensation badge (the icon looks like a tic-tac-toe grid): ![]() To save a matrix to its own stand-alone file, use the Matrix Editor. Whether compensation comes from your data as Acquisition-Defined, or is generated via FlowJo’s compensation wizard, the resulting matrix of values will be stored in XML in the FlowJo workspace document.
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