Hello SunSun,
This can be done through xinteract advanced option
-c<conservative_level> [specify how conservative the model is to be in
number of standard deviations from negative mean
to allow positive model to cover
(default 0, higher is more conservative)]
If you are using Petunia to launch TPP this option would be under
PeptideProphet options
Enter additional options to pass directly to the command-line (expert use
only!)
For example to set a CLEVEL of 1 you would put -c1 in that box. The CLEVEL
can be positive or negative. There is currently no automated way to detect
the agreement between the DECOY and model estimates. This could be done
with some works to set the -k when using ProphetModels.pl (currently not
possible through Petunia so you will need to use the commandline), which
will keep intermediate table output files. You can then compare the
appropriate columns in those files in a quantitative fashion using a tool
like R.
Cheers,
-David
On Sat, Feb 21, 2015 at 10:50 AM, zeyu sun <[email protected]> wrote:
> Hi David,
> Can you show us how to set CLEVEL threshold in TPP pipeline?
> From your link provided, the default CLEVEL is set to 0, so when
> the model estimated error-rates is different from DECOY-estimated
> error-rates, shall I set the CLEVEL to 1?
> Another silly question is, is there anyway to quantitatively estimate how
> much the model estimated error-rates differ from DECOY-estimated
> error-rates? other than comparing them in the plots......
>
> SunSun
>
> On Saturday, February 21, 2015 at 3:39:45 AM UTC+8, David Shteynberg wrote:
>>
>> Support of MSGF+ may not be full. There exist known issues with the way
>> MSGF+ encodes some modifications in pep.xml that may not be correct. Also,
>> high-scoring DECOY have been observed in MSGF+ analysis. The users are
>> encouraged to be vigilant in comparing model estimated error-rates to the
>> DECOY-estimated error-rates to make sure the two agree and set CLEVEL
>> parameter accordingly see: http://tools.proteomecenter.
>> org/wiki/index.php?title=TPP:Frequently_Asked_Questions#
>> What_is_CLEVEL_and_when_do_I_use_it.3F
>>
>> On Fri, Feb 20, 2015 at 7:59 AM, Jason Winget <[email protected]> wrote:
>>
>>> The best thing to do is to investigate the model plots to make sure that
>>> the results look accurate. In my experience, MSGF+ tends to be somewhat
>>> overaggressive and will assign peptides to some spectra that are clearly
>>> incorrect. This is usually corrected or eliminated if the results are
>>> combined with those of a second search engine (e.g. Comet) and processed
>>> with iProphet.
>>>
>>>
>>> On Thursday, February 19, 2015 at 2:49:16 AM UTC-8, Florian wrote:
>>>>
>>>> Hej.
>>>> Thanks for the comment. I analyzed my data with MSGF+ and the result
>>>> looks fine. I am just concerned that if I want to publish data which were
>>>> analyzed combining MSGF+ and TPP, I will get problems. So, could the TPP
>>>> developers please comment on the warning? Is it planned to thoroughly test
>>>> the MSGF+ any time soon?
>>>>
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>>
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