works in / but doesn't work in /home/~username/

when I put the omeka files in the server root which in my case is /htdocs/omeka/ it works but when I put it in the user's home directory, in this case /home/pfyfeomeka/public_html/omeka/ then I type in the url on my browser ( I get this displayed on the screen: The requested URL /home/pfyfeomeka/public_html/omeka/index.php was not found on this server. and this from the server log: [error] [client] File does not exist: /htdocs/home
which indicates that it is looking in the server root for the files.
this happens when my rewrite base is commented out or when I have:

RewriteBase /home/pfyfeomeka/public_html/omeka

also tried

RewriteBase /home/pfyfeomeka/public_html/omeka/


RewriteBase ~pfyfeomeka/omeka

Have you tried your last one, but with leading and trailing slashes?

RewriteBase /~pfyfeomeka/omeka

Note that you'll need to do the same thing in install/.htaccess, but appending /install/ to the end.

yes it works with the trailing slash