Ludovic,
Go ahead and post the files to the newsgroup's file area
(http://groups.google.com/group/spctools-discuss/files), and hopefully
one of the validation experts will take a look.
I will point out that PeptideProphet uses random initialization for
it's curve fitting (EM algorithm). So it's
It's is hard to say from your description exactly the problem with the
analysis. The order of files given to xinteract should not affect
results. Something is certainly not right in the analysis. If you
post your files I can tell you more.
-David
On Tue, May 18, 2010 at 4:35 AM, lgillet wrote
Hi everybody,
I recently encountered a "bug" I think when people in my lab installed
the newest TPP (v4.3 JETSTREAM rev 1, Build 201004201202 (linux)),
especially when I try to confront the result to v4.0 which was our
former "benchmark" version.
When searching the same 4 pep.xml files with v4.0 an
