Hello Jason, In an earlier version of iProphet FPKM message was being printed erroneously. Does the peff database actually contain "FPKM=" in the description? If the FPKM model was actually used you would have an FPKM model reported in the pepXML file and the models viewer should display it.
Cheers, -David On Mon, Apr 4, 2016 at 7:16 AM, Jason Winget <[email protected]> wrote: > I've done several searches using the nextprot_all peff database from > ftp://ftp.nextprot.org/pub/current_release/peff/ > > At the iProphet step I see the message that the FPKM model is being > activated: > > FPKM values are available, to disable rerun with option NOFPKM ... > > > This is probably due to the overloading of the ID line in the PEFF format > to include mods & sNPs triggering whatever parse rules are used to find > FPKMs. > > It's not a big deal to include the NOFPKM flag for now, but it may be > useful in the future to refine the automatic parsing of FPKM values. > > -- > 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 https://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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
