Hello James, Yes, these values are still hard-coded. If you wish to test alternative values, you can edit lines 958-959 and recompile:
https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp MIN_WT = 0.5; MIN_PROB = 0.2; Let us know if you find anything interesting! Cheers, --Luis On Wed, Dec 23, 2020 at 3:04 PM James Go <[email protected]> wrote: > Hi Luis, > > Is this option still hardcoded in the most up to date version of > ProteinProphet? > > On Tuesday, November 22, 2011 at 5:39:54 PM UTC-8 Luis wrote: > >> Hello Xiao, >> You are correct: there is a lower limit in ProteinProphet to disregard >> peptides below a certain probability and assigned weight. These values >> (0.2 and 0.5, respectively) are unfortunately hard-coded in the program and >> cannot be set by the user; in order to change them you would have to alter >> the code and recompile the software. >> Cheers, >> --Luis >> >> >> On Mon, Nov 21, 2011 at 8:23 AM, Xiao <[email protected]> wrote: >> >>> Dear all, >>> >>> I have a question about the ProteinProphet. From the link of "More >>> Analysis Info" in the ProteinProphet results view window, I found the >>> "min peptide probability" to be 0.2. Is 0.2 the probability threshold >>> that ProteinProphet uses to select the peptides? If yes, can I set a >>> different value (if necessary)? >>> >>> Thanks, >>> >>> Xiao >>> >> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >>> >> -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/6417474e-9e5f-4974-8ecf-ad508d022727n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/6417474e-9e5f-4974-8ecf-ad508d022727n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CACyS9bp0VKuhiRURhKLB6Urvsis9t-6QLvLVX%3Dh5At5S%2Bh3vcA%40mail.gmail.com.
