Hi David and Magnus, Thanks for sharing the details, I will give it a try and let you know how it works for me.
Best, Chih-Chiang On Tuesday, December 9, 2014 12:35:26 PM UTC-5, magnus....@gmail.com wrote: > > Hi David and Chih-Chiang, > > The recent question was about modifications, which can in principle be > treated as different amino acids (which is exactly what they are). For > RTCalc and similar models, each modification needs to be present in 15-20 > or so distinct peptides for the coefficients to start to converge [and > RTCalc needs at least 80 peptides, although 51 (?) are mathematically > sufficient]. > > FYI, I uploaded a Taverna workflow for PeptideProphet pepXML to RTCalc > based on a default TPP installation on Windows: > http://www.myexperiment.org/workflows/4042.html. This also contains the > calls to RTCalc. I'd be curious to know if you can run it and what you > think about it! You need R and Rserve (for the statistics and plots) and > Taverna workbench to run the workflow, but that should be it. > > > Cheers, > > Magnus > > > > On Monday, 8 December 2014 20:36:33 UTC+1, David Shteynberg wrote: >> >> 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 >> <chihchi...@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 >> >> >>>>>>> >> >> >>>>>>> -- >> >> >>>>>>> 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-discu...@googlegroups.com. >> >> >>>>>>> To post to this group, send email to >> spctools...@googlegroups.com. >> >> >>>>>>> >> >> >>>>>>> Visit this group at >> >> >>>>>>> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >>>>>>> For more options, visit >> https://groups.google.com/groups/opt_out. >> >> >>>>>>> >> >> >>>>>>> >> >> >>>>>> >> >> >>>>>> >> >> >>>>> -- >> >> >>>>> 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-discu...@googlegroups.com. >> >> >>>>> To post to this group, send email to >> spctools...@googlegroups.com. >> >> >>>>> Visit this group at >> >> >>>>> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >>>>> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >>>>> >> >> >>>>> >> >> >>>> >> >> >>>> >> >> > -- >> >> > 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-discu...@googlegroups.com. >> >> > To post to this group, send email to spctools...@googlegroups.com. >> >> > Visit this group at http://groups.google.com/group/spctools-discuss. >> >> >> > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > 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-discu...@googlegroups.com. >> > To post to this group, send email to spctools...@googlegroups.com. >> > Visit this group at http://groups.google.com/group/spctools-discuss. >> > For more options, visit https://groups.google.com/d/optout. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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