Hi Chih-Chiang,
You are correct, I just checked the code and the PEPXML option has the
following comment I left there in the code:
if (!pepxmlfile.empty()) {
//TODO: DDS Implement rtcalc->parse_pepXML(pepxmlfile);
return 0;
}
So I haven't implemented that feature yet and should remove it from
the usage statement. However, you should still be able to get
results by pasting a list of peptides and RTs in two columns. The
tool has two different training modes. The basic mode uses a linear
regression model based on peptide properties, the ANN model uses an
artificial neural network based on peptide amino acid positional
information and other peptide properties. They are different learning
algorithms.
-David
On Fri, Dec 5, 2014 at 9:36 AM, Chih-Chiang Tsou
<chihchiang.t...@gmail.com> wrote:
> Hi David,
>
> I am trying to use rtcalc to train a prediction model directly from PepXML.
> Is the option "PEPXML" for that? it didn't work for me.
> Another question is what's the difference between coefficient file and ANN
> model file?
>
> Thanks,
> Chih-Chiang
>
>
> On Tuesday, April 23, 2013 12:29:18 PM UTC-4, magnus....@gmail.com wrote:
>>
>> Yep - this works fine, thanks!
>>
>> Cheers,
>>
>> Magnus
>>
>> On Wednesday, 17 April 2013 17:49:46 UTC+2, magnus....@gmail.com wrote:
>>>
>>> Hi David,
>>>
>>> Somehow I missed your reply (which was very quick). I will give it a try
>>> now - thanks!
>>>
>>>
>>> Magnus
>>>
>>> On Thursday, 28 March 2013 22:28:34 UTC+1, David Shteynberg wrote:
>>>>
>>>> Thanks for the files you've provided. I was able to find and fix one
>>>> error in the code. TPP revision 6171 from trunk should contain this fix.
>>>> Also I found an error in your commands. When you train a a Neural Net with
>>>> RTCalc you have to use the ANN= option if you want to then apply the
>>>> trained
>>>> model to data. Here are my commands on your files using my new code:
>>>>
>>>>
>>>> RTCalc TRAIN=list2_predictions_no_neg.txt ANN=list2_ann_DDS.coeff
>>>>
>>>>
>>>>
>>>> RTCalc PEPS=peptides.txt ANN=list2_ann_DDS.coeff
>>>>
>>>> I hope it works for you too!
>>>>
>>>> -David
>>>>
>>>>
>>>>
>>>> On Thu, Mar 28, 2013 at 10:58 AM, magnus....@gmail.com
>>>> <magnus....@gmail.com> wrote:
>>>>>
>>>>> OK - I sent the training set and the ANN model by e-mail.
>>>>>
>>>>>
>>>>> On Thursday, 28 March 2013 18:49:41 UTC+1, David Shteynberg wrote:
>>>>>>
>>>>>> Hi Magnus,
>>>>>>
>>>>>> Can you forward me the files you have and the commands you are using
>>>>>> and I will debug?
>>>>>>
>>>>>> Thanks,
>>>>>> -David
>>>>>>
>>>>>> On Thu, Mar 28, 2013 at 10:47 AM, magnus....@gmail.com
>>>>>> <magnus....@gmail.com> wrote:
>>>>>>>
>>>>>>> Dear All (especially David),
>>>>>>>
>>>>>>> I am trying to use the ANN retention time predictor. The training
>>>>>>> runs OK, but when trying to use it I get this error:
>>>>>>>
>>>>>>> gsl: init_source.c:29: ERROR: vector length n must be positive
>>>>>>> integer
>>>>>>> Default GSL error handler invoked.
>>>>>>>
>>>>>>> This application has requested the Runtime to terminate it in an
>>>>>>> unusual way.
>>>>>>> Please contact the application's support team for more information.
>>>>>>>
>>>>>>>
>>>>>>> I used ca. 60,000 different peptides in the training set. How many
>>>>>>> would be needed? What are the things to look out for?
>>>>>>>
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Magnus
>>>>>>>
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>>>>>>
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>>>>
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