The Batch function is meant to perform a simple repetitive command across a large number of files.
Whereas the Edit utility is a powerful and general editor tool, the Batch function is intended to solve some very specific, yet common edits. These include adding new keywords, deleting keywords and changing the dates in files. These four functions are intended to be quick solutions to common problems.
When the Batch button is press in the main window, you are asked to identify a folder. The FCS files in that folder. Note that there is no way to add more files to the batch window once it is open, so you need to have all of your files moved to a common folder to run this tool effectively.
Each of the batch commands has a checkbox to turn it on or off. The Run button will execute each of the enabled batches. Click on any of the sections below to scroll to the section explaining it.
This command provides the ability to insert a new keyword into your FCS files. Enter the name of the keyword in the first edit field. The value associated with the keyword in each file is made up from the Prefix, and an optional number. You can set the initial value, and the amount which the is added to the number in each sucessive file.
Example: with the settings shown in the dialog above, ProJo will insert /SampleID/99-01-000 in the first file, followed by /SampleID/99-01-001, etc.
To enter the same value for the keyword in each file, simply leave the Increment By and Start At fields empty.
Many labs think they are pretty clever coming up with elaborate naming conventions to encode all sorts of patient, cell line, date and other information in the name of the file as they collect it. The problem is that this is cumbersome to work with, prone to error, and most importantly excludes information from your analysis software, which may be able to use that data.
This function will read the file name of each file and extract a substring of the name. In the example above, if the folder Experiment (as show in the window title) were to contain the file: 19990204-23499-341.fcs, then if would insert /PatientID/23499/ into the header of the FCS file.
This function simply removes the keyword and value from the FCS Header. It is useful expecially in privacy protection. Note that unlike most other editing functions in ProJo, you cannot Undo this operation. If you use the Overwrite option, the information is irretrievably lost when you run this function.
Because of Y2K issues, there will shortly be many cytometers running with their clocks set wrong. With this function ProJo provides a quick way to reset the time within your files, by adding a set number of years to the $DATE field in each file.
Experts recommend setting clocks back to 1972, so that any day of week computations will result consistent to the year 2000. So the default value of how much to add to files in 28 years.
The current version of CellQuest (TM) does not correctly write dates in the years 2000 and beyond. They are truncated down to one digit. ProJo will repair this defect, yielding four digit dates. [CellQuest is a trademark of Becton Dickinson and Company, who spent more on Y2K compliance than Tree Star's total operating expenses, and they still didn't get it right.]
Next to the Run button is an innocuous little check box that is labelled Overwrite. When checked ProJo will write the results of its batch operations over the existing files. Be careful using this option. It is much safer to write the results to new files, and once you are confident of the results, then delete the original. But in the case of large files it can be unpractical to duplicate all of the data, so this option will limit the amount of space required to run the operation.