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
> <[email protected] <javascript:>> 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, [email protected]
> wrote:
> >>
> >> Yep - this works fine, thanks!
> >>
> >> Cheers,
> >>
> >> Magnus
> >>
> >> On Wednesday, 17 April 2013 17:49:46 UTC+2, [email protected]
> 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, [email protected]
> >>>> <[email protected]> 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, [email protected]
> >>>>>> <[email protected]> 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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