There's got to be a better way!

OK, getting on a soapbox here.

I just want my data. For all of the standardization and formatting that the FCS file standard is providing, when I open files up in flow cytometry analysis software, a myriad of annoyances present themselves... variously, at one point or another:

1) parameters show up out of order

2) parameters aren't labeled with the reagent or dye

3) only the scatter parameters show up

etc etc

A skeptic might say, "maybe it's just a you issue" or "maybe it's just a skill issue;" some helpful soul might provide helpful advice about settings on my analysis software or settings on my instrument. Sure, there is probably a fix... but honestly, sometimes, I want to work with my data outside of flow cytometry software, and in those settings, there is a universal, easy standard... a bloody CSV file. Why can't we just get an option to export from the instrument as a CSV file? Why don't we just work with CSV files from the start?

I know that there is likely a reason that I'm not appreciating... something about the FCS header containing all kinds of information, or the size of the files, or something else. The annoyance doesn't seem to be worth whatever the FCS format is providing, though.

Today, I learned from an interesting LinkedIn post that there are two ways to order data, which is used for an FCS file is indicated in one of the header parameters. You're fine if you use flowCore in R to import your data, but you might want to know about an independent way to import data without relying on the flowCore library and if you go the DIY path, you better understand byte order.

That's helpful, and I'll keep that in the back of my head, but it also made me think that things are way overcomplicated. If I could get - straight out of the machine - a column for each fluorescence and scatter channel, and a row for every cell, I wouldn't have to bother with the right prep. I could just jump right into looking at my data. Tell me why that can't happen in the comments, or - if you're an instrument manufacturer - tell me that the next version of your acquisition software will do this. Soothe my angry brain, LOL.