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3 Advantages FCS Express 6 Has Over Other Flow Cytometry Data Analysis Software Programs

Written by Tim Bushnell, PhD

After running a flow cytometry experiment and collecting the data, the first and only thing any scientist wants to do is analyze the data.

To do this properly in the field of flow cytometry, a quality data analysis software program is required.

The problem is, most of the current data analysis programs are archaic, clunky, or overly complex. The package or packages that were useful in the 1990s have not been updated properly and, as a result, are buggy. Worse, they often require a great deal of training to use correctly.

However, the biggest problem overall with the majority of the data analysis software programs available is their outdated workflow.

For example, most of these programs require you to follow this sequence: load your data into the software program, perform your gating and analysis in the software program, and then spend an immense amount of time exporting your data to PowerPoint, Excel, Prism, and so on, and then further analyzing your data.

…and further analyzing your data, and further analyzing your data, and further analyzing your data…

The Complexity Of Most Data Analysis Software Packages

Why does analyzing flow cytometry data need to be this complex?

Why is there so much busy work involved?

Think about it – in most of these flow cytometry data analysis packages, you first have to do your analysis in that software program, then, as mentioned, you have to export to a different software program like Excel, and then you have to do more data analysis in that software program (i.e. applying Excel shortcuts and equations), then you have to generate your bar charts, pie charts, and whatever else you need, in Excel too.

Wait, there’s more… then you have to copy and paste your charts into yet another software program, such as PowerPoint or Illustrator, not to mention the back and forth you have to do in order to move the raw data from one software program to another. It’s a tiresome and needless process.

At the end of all this, you have your original flow cytometry data files open, as well as dozens and dozens of individual flow plots (at least!), workspace windows, tables, layouts, Excel and PowerPoint files, Prism, .CSV files, and more.

All of these items remain open on your computer because you have to keep them open in order to go back and forth to adjust your analysis.

There’s no reason for it.

What Scientists Want From A Data Analysis Software Program

Data analysis is about producing a final result.

The final result, in this case, is the Excel spreadsheet, or the table, graph, or overall figure you need for your presentation, paper, or grant.

The final result is not 250 flow plots stuck in a workspace.

As such, the ideal software analysis program would allow you to analyze all of your data in a single program. In other words, the ideal software program would allow you to open up an Excel-like table and a PowerPoint-like layout directly in the software program. It would allow you to utilize all of the Excel shortcuts and equations directly in the program itself.

The ideal software program would make it so you didn’t have to constantly export your data to other software programs, or keep dozens and dozens of plots open just in case you need to slightly modify a gate.

Why can’t you just modify your gates within a PowerPoint-like layout and have all of the downstream gates, plots, tables, T-tests, P-tests, numbers, and analyses automatically updated in an instant?

Most importantly, the ideal software program would be simple to use. Instead of requiring complex training, it would be streamlined and as easy to use as Excel or PowerPoint.

3 Advantages Of The FCS Express 6 Data Analysis Program

If you’re using one of the more outdated and complex data analysis software packages on the market, you might want to think about making a change.

This is usually as simple as asking your Principal Investigator or Institution Administrators to update their current software license to something more modern (and more affordable) like FCS Express 6.

If they ask you to justify the change, simply send them the following list…

1. FCS Express 6 is the most user-friendly data analysis program on the market.

If you can use Microsoft Excel or Microsoft PowerPoint, you can use FCS Express 6…

The world of flow cytometry data analysis has changed immensely over the years. It wasn’t that long ago that only core managers, with years and years of training, were the only ones able to analyze flow cytometry data correctly.

This is why most of the data analysis software packages on the market are overly complex. It’s because these packages were created for the top 1% of core managers, not for end users and most core managers.

FCS Express 6 is different. I’ve found this program is ideal for not only core managers, but for end users as well.

The best thing about this program is that anyone, even the most novice flow user, can walk up to it and start creating plots in seconds. This just isn’t the case with other software programs on the market.

I’ve seen even the most novice user sit down, open up an FCS Express 6 PowerPoint-like layout, drag in a data file, watch the plot automatically open up, and then very quickly start doing some very advanced analyses.

2. The FCS Express 6 workflow is modern and aligned with current best practices.

As mentioned above, the workflow of most data analysis software programs is overall complex at best, and flat-out wonky at worst.

Why should I have to load all of my files into some workspace, open dozens and dozens (sometimes hundreds!) of individual plot windows to draw my gates, then open the program’s supplementary tables and layouts, and then export to Excel and PowerPoint, and then go back and forth for hours and hours (or even days) tweaking each individual gate in each individual plot, while simultaneously updating my exported files with every single tweak?

It’s exhausting.

The larger problem here is that this outdated and complicated workflow can result in data analysis errors and experimental irreproducibility. It’s just not feasible to expect new flow cytometry users, or any user for that matter, to mentally keep track of every single change in every single individual plot window, every single time a change needs to be made.

With FCS Express 6, however, any user, new or advanced, can simply just open up the program’s PowerPoint-like layout and Excel-like table and start creating plots, tables, charts, T-tests, P-tests, and everything else, right in the program itself… all the way to completion of whatever flow table or figure you need for your paper or grant.

The best part is, every change made to any gate in any plot results in everything downstream being automatically updated.

Each and every plot is already in a single PowerPoint-like layout, not in dozens and dozens of individual plot windows. This means you can see these changes happening across the board in real-time.

3. FCS Express 6 has the most rigorous quality control standards.

There’s a reason that why Express 6 is used in more flow cytometry clinical analyses than any other data analysis package.

FCS Express 6 has more than 100 reference labs using the clinical version, including 3 of the world’s largest laboratory companies (Labcorp, Quest, and Genoptix).

FCS Express 6 also provides an IQ/OQ package for validation. IQ stands for Installation Qualification and OQ stands for Operational Qualification.

If, for example, you are a pharmaceutical company who is acquiring a new piece of equipment, you will need to design specifications that define exactly what’s in that piece of equipment. This is where the IQ/OQ package comes in.

Finally, FCS Express 6 also provides comprehensive 21 CFR Part 11 compliance features. The Food and Drug Administration’s (FDA’s) Electronic Records and Electronic Signatures Rule (“Part 11”) defines the requirements for submitting documentation to the FDA in electronic form, as well as criteria for use of electronic signatures.

FCS Express 6 meets these requirements and is designed to maintain both the machine-readable metadata and human-readable reports.

FCS Express 6 has the following features that can enhance your lab’s Part 11 compliance program: security, access limitations, authority checks, record protection, audit trails, electronic signatures, and much more.

In fact, over 300 independent security permissions can be set for each security group, giving you tremendous flexibility in defining your own access limitations.

Overall, FCS Express is the ideal data analysis software program to use when analyzing your flow cytometry experiments because it is the most user-friendly program available that is both aligned with current data analysis best practices, and maintains rigorous quality control standards.

To learn more about FCS Express 6, go to the FCS Express 6 informational page. 


To learn how to get a free FCS Express license, and to get access to all of our advanced materials including 20 training videos, presentations, workbooks, and private group membership, get on the Flow Cytometry Mastery Class wait list.

Tim Bushnell, PhD


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