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 >>>>>> >>>>>> -- >>>>>> 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 [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> >>>>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
