Ah yes...it was a bug I meant to fix ;) Thanks for testing! On Mon, Apr 4, 2016 at 7:46 AM, Jason <[email protected]> wrote:
> I can't find the string "FPKM=" anywhere in the database, so perhaps it's > an erroneous message. > My version is TPP v5.0.0a5 downloaded on 3/10/2016 > > On Mon, Apr 4, 2016 at 10:39 AM, David Shteynberg < > [email protected]> wrote: > >> 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 a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/uO9Wdd_CjDI/unsubscribe >> . >> To unsubscribe from this group and all its topics, 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. > -- 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.
