In general, RTCalc should be able to handle modified peptides
separately from the unmodified peptides. That said, learning
algorithms such as this perform best when trained with enough data.
If modified peptides are only a small part of the set they may not be
very well characterized by the algorithm.
-David
On Sat, Dec 6, 2014 at 12:33 PM, Chih-Chiang Tsou
<chihchiang.t...@gmail.com> wrote:
> Hi David,
>
> Thanks for the reply, does the model take modification into account or it's
> based on only sequence? And should I remove modified peptides from training?
>
> Thanks
> Chih-Chiang
>
> On Friday, December 5, 2014 1:25:38 PM UTC-5, David Shteynberg wrote:
>>
>> 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
>> <chihchi...@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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