What are the differences between PE and ELF binary formats?

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What is the difference between Windows PE binary and Linux ELF binary formats? How does a compiler convert a file into the specified format of the operating system when it should only create the assembly language equivalent of the source code? Could somebody explain in brief?

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TJD On BEST ANSWER

PE and ELF are just different formats for describing similar information. Neither of them "access the processor". Both just contain information that is used by an OS to load binary executables. The processor doesn't really care how executable code gets loaded.