Dear Assa,
I am having a problem building a ROC curve with my data using the ROCR package. I have 10 lists of proteins such as attached (proteinlist.xls). each of the
your file didn't make it to the list.
lists was calculated with a different p-value. The goal is to find the optimal p-value for the highest number of true positives as well as lowaest number of false positives.
As far as I understood the explanations from the vignette of ROCR, my data of TP and FP are the labels of the prediction function. But I don't know how to assign the right predictions to these labels.
I assume the p-values are different cutoffs that you use for "hardening" (= making yes/no predictions) from some soft (= continuous class membership) output of your classifier.
Usually, ROCR calculates the curves as function of the cutoff/threshold itself from the continuos predictions. If you have these soft predictions, let ROCR do the calculation for you.
If you don't have them, ROCR can calculate your characteristics (sens, spec, precision, recall, whatever) for each of the p-values. While you could combine the results "by hand" into a ROCR-performance object and let ROCR do the plotting, it is then probably easier if you plot directly yourself.
Don't be shy to look into the prediction and performance objects, I find them pretty obvious. Maybe start with the objects produced by the examples.
Also, note ROCR works with binary validation data only. If your data has more than one class, you need to make two-class-problems first (e.g. protein xy ./. not protein xy).
BTW, Is there a way of finding the optimum in the curve? I mean to find the exact value in the ROC curve (see sheet 2 in the excel file for the ROC curve).
Someone asked for optimum on ROC a couple of months ago, RSiteSearch on the mailing list with ROC and optimal or optimum should get you answers.
I would like to thank for any help in advance
You're welcome. Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
