Thank you for the very clear explanation. I was just a bit confused
about how many proteins you can quantify and instead how many can be
significantly different. After your confirmation that all the
parameters that I used were correct I will look more into details of
my data. Do you know if there
Without looking at your data directly it is hard for me to comment on
the quality of the results. It sounds like everything is working
correctly. The reduction in the protein count when you filter by
ASAPRatio p-value is to be expected since p-value represents a
likelihood that a given protein's
I forgot, another little question: at the end of the protProph
analysis I can't see the protein name (but can see just the accession
number) when I work with the IPI database; while I can see everything
correctly if I use for example the UniprotKB database. Is there some
parameter to change in the
Hi David,
yes I analysed quite a big set of data (16 LC runs) and it seems to
work. But I have to look better into the results. The first thing that
impressed me is that after I analysed and validated this set of data,
the output of proteinProphet is more or less 1000 proteins (after
setting min p
Hi Federico,
Your parameter set looks correct. Have you tried to execute to
program with this set of params? Did it seem to work?
-David
On Mon, May 18, 2009 at 6:32 AM, fto...@gmail.com wrote:
>
> Hope not to be too annoying cause I am really enjoying this toolbox
> but I have always lot of
