There may be instances where you would want to export your data from OMIQ. For example, you may want to export the coordinates of a dimension reduction task or the gating information for each cell/event and run a parallel analysis outside of OMIQ. OMIQ allows for the export of data as either CSV file or FCS file.
If you want to export statistics from OMIQ, please see our support article on Export Specific Statistics per Filter(s).
1. Add an Export Data Task
Click Add new child task and select Export Data from the task selector.
2. Setup the Export Data Task
2.1 Select Files and Features
Select the Files you want to export. Select the Features that you want to include in the exported file. Note that features will be added as columns in your exported file.
2.2 Enter Export Data Settings
Format: Choose between CSV or FCS file to export.
Concatenate File: Select this option if you want to concatenate the files into 1 file.
Fill Missing Columns: Select this option if you want to add a column for a missing feature in a file. OMIQ will automatically populate those columns with "0".
Select Filters (Optional): In OMIQ, gates are called filters. If you want to add in any gating information, select the filters here.
In the event that a row belongs to multiple filters, OMIQ labels the row as belonging to the filter with the smallest count. OMIQ can only display one filter at a time.
If you are exporting a CSV file, OMIQ will add a column to your file labeled as OmiqFilter column displaying the filter name.
If you are exporting a FCS file, the OmiqFilter column will contain numbers (i.e. 0,1,2,3 and so on). The zip file containing the exported data will contain a CSV file labeled "_FilterValuesToNames" which contain the legend to what the numbers represent.
Drop rows not found in any selected filters: This option automatically excludes rows that are not found within the selected filters. The default is that this option is selected. Deselect this if you want to know if a row is negative for the selected filters.
Filter Name Format: You can choose how OMIQ displays the filter name either as Default or Full Path. Default lists down just the filter name while Full Path would list down the full gating path.
Reduce Precision (to reduce file size): This option allows you to choose how many precision digits are written by OMIQ. You can choose to write the original precision digits (Keep Orig Precision), 3 precision digits (Keep 3 Prec Digits), or 4 precision digits (Keep 4 Prec Digits).
Add Original Row Number: Adds the row number based on the original data to the file.
Exported Data Units: This option relates to how the values for features are exported out. Scaled per Scaling Settings allows you to export the scaled values of the features using the scaling task available in the workflow. Original ("raw") allows you to export the original "non-scaled" values of the features
2.3 Run
Click Run Export Data. This will take you to the Status tab and you can watch the progress. However, you are free to go back to your workflow or do whatever you please while this runs in the cloud. The status can also be seen in the Workflow itself, or you can have an email sent to you when it is completed.
3. Download the Results
Go to the Results tab and download the zip file containing the exported data.