Some people are having trouble with Firewire-based audio interfaces and scanners with El Capitan.
Opening a search engine and entering "firewire deprecated el capitan" yields plenty of instances.
Here is some text from an article I archived:
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Note: Literally the second I filed this column, I received an email from Apogee Electronics stating that its Ensemble hardware, an expensive and highly regarded audio interface, will not be supported on Mac OS X 10.11 El Capitan. This interface was discontinued less than three years ago and cost roughly $2,500 new. I own one. It used to be that when you bought expensive audio production hardware, you expected more than a few years of use.
But don't be so quick to blame Apogee. With El Capitan, Apple has discontinued development and maintenance of its FireWire Core Audio driver, which will cause problems with a huge number of other hardware devices as well.
source:
http://www.infoworld.com/article/2988096/mac-os-x/sorry-unix-fans-os-x-el-capitan-kills-root.html
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I have an external firewire400 drive I've used with El Capitan (even booted using it for a while), along with a couple of firewire800 backup drives, and all still run well enough...