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Binary (Raw Data) is one of the formats available for putting files on another computer. If this format is chosen, the data part of the Macintosh file will be uploaded without any interpretation or conversion.
Most Macintosh programs create files with all their information in the data part (such as StuffIt, Microsoft Excel, Microsoft Word). Similarly, most cross-platform standard file formats (such as GIF and JPEG image formats, and virtually every sort of file used on the World Wide Web) use only the data part. In these cases, using the Binary (Raw Data) format is a simple way to transfer files that does not result in information getting lost.
However, some Macintosh files include a resource part, and that information will be lost if you use Binary (Raw Data) format. If the file contains important information in its resource part, and will be retrieved only by a Macintosh, Zip Archive format should be chosen instead.
In most cases, the Automatic upload format will choose the correct format for your files and you do not have to worry about choosing a specific one.