Hi Rebekah, This option is still listed as "experimental", but we will try to add it to Petunia for the next release. Your hunch to use the "-w" string in the additional command-line options was on the right track; unfortunately, this page uses another program to run ASAPRatio (called xinteract), and thus the parameter format will not work for this case.
For the time being, your best option will be to run the tools up to PeptideProphet via Petunia, then switch over to the command-line to run ASAPRatioPeptideParser (with desired parameters) on the interact.pep.xml file via the command-line. To find out what parameters to use, simply type "ASAPRatioPeptideParser " in the command-line to get a usage statement. You can then go back to Petunia to run iProphet, ProteinProphet, etc after this is done. Cheers, --Luis On Mon, Mar 5, 2012 at 1:46 PM, Ruby <[email protected]> wrote: > Hi- > I currently use ASAPRatio to quantify SILAC samples. I have TPP 4.5.2 > and would like to try WaveletQuant. I see in the instructions that it > can be implemented by using ASAPRatioPeptideParser -w command line > option. However, can I use the TPP via Petunia GUI to do this? I don't > have experience using TPP via command line. I tried typing in "-w" > into the box under PeptideProphet options "Enter additional options to > pass directly to the command-line (expert use only!)", but this didn't > seem to do anything different. I don't see a place under ASAPRatio > Options for this. Any help would be appreciated! > > Thanks! > Rebekah > > -- > 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 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.
