They are inherently different measures. Probability measures the likelihood that a protein was seen based on the matched peptide evidence. The confidence measure is a lower bound estimate that takes a different approach and considers the proteins identified and among these the numbers and qualities of peptides seen, it then builds a model based on the number of peptides you would expect by random chance to hit a protein of a given length. Intuitively, a protein can have a low confidence but high probability if it is very long and has some high scoring peptides matching to it.
-David On Mon, Feb 24, 2014 at 5:33 PM, Maryam Afkarian <maryamafkar...@gmail.com>wrote: > How can a protein identification from prot.xml have a very high > probability (e.g. 1) but a low confidence (e.g. 0.295 from a real example)? > > > -- > 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-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss. > 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-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
