-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, proteins are synthetised from transcripts, not from genes, so I wouldn't use gene DE. It can become quite tricky to interpret these for some alternative transcripts. Beast, Leonor. On 28/07/12 18:06, i b wrote:

Hi, I am a bit confused about two outputs of cuffdiff: If I want to see if two samples, e.g. treated and un-treated express similar protein levels, what would be best to look at gene differential expression or transcript diff. expression?

Thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

- -- Leonor Palmeira, PhD Phone: +32 4 366 42 69 Email: mlpalmeira AT ulg DOT ac DOT be http://sites.google.com/site/leonorpalmeira Immunology-Vaccinology, Bat. B43b Faculty of Veterinary Medicine Boulevard de Colonster, 20 University of Liege, B-4000 Liege (Sart-Tilman) Belgium -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iQEcBAEBAgAGBQJQFBCdAAoJEKquFGwgRb3zchgH/3bGHlV4igMxp3eDhUCRPK5m Fa1I5Y7fvlSZXCPVjiwpoO1j6uXSiYnNYxGTPWYet4qaTKHee0lRtfPLbXhpC4t+ BgEh8HaCoruUStM9qOG/d0ljWjEwM0QRdw1/oWVvF1mLwYq+LBIZdAw0yR/9bTYo xvdmd7Qd+bDq/vh8vR4gn/Cr6oOoB16eMz++X+DXk7pUuQXXxuACt7TEU4tf5Isz ZzlpjVt0a5Y1tYuc5MA4zuhDZzB6u3NEAMzufz3VDgVx/QCX7hKQkSi6rYBaRAmu EdPnLwvVQhOcqaSGz9wSdkkeTHVcE5gmkJ8ZV6re3jua4iI9vW9Lf4ifPQCXamU= =9Frm -----END PGP SIGNATURE-----