Re: [spctools-discuss] Problem with PTMprophet

2023-04-29 Thread felipe velasquez 
Thanks Luis for your quick response. Finally, I could resolve the problem.
As a beginner user, I made a mistake with Comet params. Thanks again for
your attention and support.

kind regards,

Felipe

El vie, 28 abr 2023 a las 16:14, 'Luis Mendoza' via spctools-discuss (<
spctools-discuss@googlegroups.com>) escribió:

> Hello Felipe,
>
> The top message seems to indicate a permissions error; perhaps the files
> under /tmp are not accessible to the Apache/web user?  Since this looks
> like a Linux install, it depends on how that part of your system is set up.
>
> The large error may or may not be related to the previous one, but it is
> telling you that the pepXML file is not valid PepXML.  There can be many
> reasons for this, so it depends on how that file was initially generated.
>
> What steps did you take to go from your Thermo raw file to this pepXML?
> Do you get any other errors or warnings before this step?  Have you been
> able to run other data as a test of your TPP install?
>
> Cheers,
> --Luis
>
>
> On Fri, Apr 28, 2023 at 11:25 AM felipe velasquez 
> wrote:
>
>> Hello luis, thanks.
>>
>> [image: image.png]
>>
>>
>> This is one of the messages... there is something I can do to fix it?
>>
>> Thanks again,
>>
>> Felipe
>>
>> El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (<
>> spctools-discuss@googlegroups.com>) escribió:
>>
>>> Hello Felipe,
>>>
>>> It is in general not normal to not find "any results" with TPP when
>>> other platforms do find some, as there is often partial, if not
>>> significant, overlap.  Typically when no results are found, it points to
>>> either bad data (presumably not in this case) or incorrect parameters
>>> (including choice of database if doing sequence searching).
>>>
>>> For your specific case, we would need to know more specifics if you are
>>> looking for help in your TPP analysis -- e.g. what kind of data you have,
>>> what components are you using, what parameters were set, etc.
>>>
>>> We do note that in some instances other software does tend to inflate
>>> the number of results provided to the user, albeit with either a very high
>>> or otherwise poorly characterized error rate.
>>>
>>> Again, without knowing specifics, it is impossible to tell what could be
>>> going on.
>>>
>>> Cheers,
>>> --Luis
>>>
>>>
>>> On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez 
>>> wrote:
>>>
 hello again

 I am trying to analyze some samples from thermo raw data, but I cannot
 find any results. However, another person analyzed the same data using
 another platform and found some results. Is this normal?


 Felipe

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>>
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Re: [spctools-discuss] Problem with PTMprophet

2023-04-28 Thread 'Luis Mendoza' via spctools-discuss 
Hello Felipe,

The top message seems to indicate a permissions error; perhaps the files
under /tmp are not accessible to the Apache/web user?  Since this looks
like a Linux install, it depends on how that part of your system is set up.

The large error may or may not be related to the previous one, but it is
telling you that the pepXML file is not valid PepXML.  There can be many
reasons for this, so it depends on how that file was initially generated.

What steps did you take to go from your Thermo raw file to this pepXML?
Do you get any other errors or warnings before this step?  Have you been
able to run other data as a test of your TPP install?

Cheers,
--Luis


On Fri, Apr 28, 2023 at 11:25 AM felipe velasquez 
wrote:

> Hello luis, thanks.
>
> [image: image.png]
>
>
> This is one of the messages... there is something I can do to fix it?
>
> Thanks again,
>
> Felipe
>
> El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (<
> spctools-discuss@googlegroups.com>) escribió:
>
>> Hello Felipe,
>>
>> It is in general not normal to not find "any results" with TPP when other
>> platforms do find some, as there is often partial, if not significant,
>> overlap.  Typically when no results are found, it points to either bad data
>> (presumably not in this case) or incorrect parameters (including choice of
>> database if doing sequence searching).
>>
>> For your specific case, we would need to know more specifics if you are
>> looking for help in your TPP analysis -- e.g. what kind of data you have,
>> what components are you using, what parameters were set, etc.
>>
>> We do note that in some instances other software does tend to inflate the
>> number of results provided to the user, albeit with either a very high or
>> otherwise poorly characterized error rate.
>>
>> Again, without knowing specifics, it is impossible to tell what could be
>> going on.
>>
>> Cheers,
>> --Luis
>>
>>
>> On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez 
>> wrote:
>>
>>> hello again
>>>
>>> I am trying to analyze some samples from thermo raw data, but I cannot
>>> find any results. However, another person analyzed the same data using
>>> another platform and found some results. Is this normal?
>>>
>>>
>>> Felipe
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discuss+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
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>>> 
>>> .
>>>
>> --
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>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
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>> To view this discussion on the web visit
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>> 
>> .
>>
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> 
> .
>

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Re: [spctools-discuss] Problem with PTMprophet

2023-04-28 Thread felipe velasquez 
Hello luis, thanks.

[image: image.png]


This is one of the messages... there is something I can do to fix it?

Thanks again,

Felipe

El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (<
spctools-discuss@googlegroups.com>) escribió:

> Hello Felipe,
>
> It is in general not normal to not find "any results" with TPP when other
> platforms do find some, as there is often partial, if not significant,
> overlap.  Typically when no results are found, it points to either bad data
> (presumably not in this case) or incorrect parameters (including choice of
> database if doing sequence searching).
>
> For your specific case, we would need to know more specifics if you are
> looking for help in your TPP analysis -- e.g. what kind of data you have,
> what components are you using, what parameters were set, etc.
>
> We do note that in some instances other software does tend to inflate the
> number of results provided to the user, albeit with either a very high or
> otherwise poorly characterized error rate.
>
> Again, without knowing specifics, it is impossible to tell what could be
> going on.
>
> Cheers,
> --Luis
>
>
> On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez 
> wrote:
>
>> hello again
>>
>> I am trying to analyze some samples from thermo raw data, but I cannot
>> find any results. However, another person analyzed the same data using
>> another platform and found some results. Is this normal?
>>
>>
>> Felipe
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/CAA35R_UNFxZW6Jw-AwszcqWP3OkxGH-BN0-tqwKn9cPLJrXyPA%40mail.gmail.com
>> 
>> .
>>
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> 
> .
>

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Re: [spctools-discuss] Problem with PTMprophet

2023-04-28 Thread 'Luis Mendoza' via spctools-discuss 
Hello Felipe,

It is in general not normal to not find "any results" with TPP when other
platforms do find some, as there is often partial, if not significant,
overlap.  Typically when no results are found, it points to either bad data
(presumably not in this case) or incorrect parameters (including choice of
database if doing sequence searching).

For your specific case, we would need to know more specifics if you are
looking for help in your TPP analysis -- e.g. what kind of data you have,
what components are you using, what parameters were set, etc.

We do note that in some instances other software does tend to inflate the
number of results provided to the user, albeit with either a very high or
otherwise poorly characterized error rate.

Again, without knowing specifics, it is impossible to tell what could be
going on.

Cheers,
--Luis


On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez  wrote:

> hello again
>
> I am trying to analyze some samples from thermo raw data, but I cannot
> find any results. However, another person analyzed the same data using
> another platform and found some results. Is this normal?
>
>
> Felipe
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/CAA35R_UNFxZW6Jw-AwszcqWP3OkxGH-BN0-tqwKn9cPLJrXyPA%40mail.gmail.com
> 
> .
>

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[spctools-discuss] Problem with PTMprophet

2023-04-27 Thread felipe velasquez 
hello again

I am trying to analyze some samples from thermo raw data, but I cannot find
any results. However, another person analyzed the same data using another
platform and found some results. Is this normal?


Felipe

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