I just committed the change. Please update from trunk, recompile
PeptideProphetParser and try it again.
Thanks,
-David
On Wed, Nov 10, 2010 at 2:12 PM, ira cooke wrote:
> Hi David,
> Thanks very much for fixing this. Would you recommend that we check
> out the latest source and just recompile
Hi David,
Thanks very much for fixing this. Would you recommend that we check
out the latest source and just recompile PeptideProphet? I guess this
would be safer than upgrading our whole TPP install to the latest
code?
We'll contact Phenyx support about the pepXML dump and hopefully they
can fi
Hello again,
I realized you sent me the db and each protein listed only once, so
the problem is with the Phenyx pepXML dumper writing these incorrect
tags. Temporarily, I have removed these entries using the sed
command: sed -i 's/^http://groups.google.com/group/spctools-discuss/web/interact.pep.
Hi Ira,
Thanks for providing your Phenyx search results. I was able to
resolve a bug in PeptideProphet, which was preventing it from reading
in any Phenyx search results. At this point I still cannot process
these files with PeptideProphet because of the alternative_protein
entries. Somehow, th
Some of the ASAP ratio values have large standard deviations. This
tends to happen when the smoothed extracted ion chromatogram and the
raw extracted ion chromatogram have large differences. Is there any
way to filter the peptides with large standard deviations in ASAPratio
prior to running Prote
