I suspect Cory will "chime in", but yes, what he is talking about is a fresh installation of OS 10.11.1. But, and I suspect he would tell you the same thing, it is critical that you have a backup to an external device first. Then, the way the process would work is as follows:
1. Boot your machine "to" the Recovery Partition.
2. Use Disk Utility there to Erase and Format your internal drive.
3. Do a fresh installation of OS 10.11.1 from there.
4. Reboot your machine.
5. Use Migration Assistant (contained within the Utilities folder inside your Applications folder to "migrate"/copy all the non-system stuff from the backup you made to the external drive.
One other thing that is very important is if you are using any third party applications, have any of them needed upgrades to work with El Capitan?
Of course, all this assumes it is not a hardware issue.