This can be very useful for sorting and analyzing the data later on. This way you are assured the correct keywords are carried forward. In fact it is highly encouraged to be adding keywords when setting up the file acquisition on the instrument. Any custom defined keywords will also appear here. To the left is a list of all the keywords that are in the file, from the instrument the data was acquired on to who acquired it and more. The output from this action is shown in figure 2. This information is only a right-click away in FJX.įigure 1: Accessing FCS header information in FJX The header information of the FCS file contains a great deal of information that is very useful to review and extract when performing quality control or troubleshooting. This article will focus on the power of FlowJoX (FJX) and provide some tips and tricks to improve the researchers’ analysis. These keywords are only the tip of the iceberg when it comes to performing advanced analytics. These include define keywords that are added to the file automatically, as well as terms that can be defined by the user. The header file contains what are termed ‘keywords’. The FCS standard divides the file into two components, the listmode file that contains the sequential data from all the detectors.
Compensation flowjo software#
Since the creation of the FCS standard, flow cytometrists have had the ability to analyze data in third party software because of the community’s agreement on the standard. fcs_file_example_import_comp_csv.Primary data analysis, that is the analysis at the sample or tube level, is where the populations of interest are identified and the necessary data is extracted for secondary analysis.( imported compensation viewed in the Cytobank interface) The more precise value is stored and used behind the scenes. 00 for values that are actually more precise. 01 percent, the values displayed in the interface will be rounded to the nearest. Also, for compensation values with resolution smaller than. Note that the compensation matrix values are displayed as percent instead of decimal. The example CSV attached to this article after upload to Cytobank. The example CSV attached to this article before upload: Cytobank also supports the import of values in scientific notation using the letter E (for example, the number 0.00119 written as 1.19E-03). For example, a CSV value of 1 is displayed as 100 in the Cytobank interface. The values in the CSV should represent decimal values (typically between 0 and 1), though they are viewed as percent values in Cytobank.The channel names must follow the same ordering in both the rows and columns or an error will occur.The following examples will all have the same effect: PE-A, PE-A::CD33, PE-A :: CD33 Spaces between the short name, double colon, and long name don't matter.
If long names are present, they must follow the short name with a double colon. Only the channel short names are required in the CSV file.An example FCS file to which the compensation applies is also attached so that this workflow can be tried out. Īn example CSV file is attached to the bottom of this article that shows the minimum required formatting for a file that gets imported as a compensation matrix. Once you arrive on the Compensation page, click the Import button, select CSV F ile and Choose file for upload. To import compensation matrices created in a different software, access the Compensation page from the Compensation tab on the experiment level navigation bar. Even if this type of export isn't explicitly supported in the software being used, copy-pasting a matrix into a spreadsheet manually and saving it as a CSV file will also work. This allows import of compensation from FlowJo or any analysis software that supports export of compensation matrices in CSV format. To support efficient downstream analysis of data using compensation matrices created in a different software, the Cytobank platform supports the ability to import a CSV file that represents a compensation matrix. However, you may want to create and modify compensations in a software other than the Cytobank platform. Compensation is a core part of most fluorescent workflows, and there are many ways to create and modify compensation matrices in the Cytobank software.
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