Hi Brian, If ASAPRatio was run on the dataset and imported to protXML at the ProteinProphet step then you should be able to see ASAPRatio ratios and p-values on the ProteinProphet page. You should then see controls to sort and filter by p-value.
-David On Fri, Sep 14, 2012 at 9:48 AM, Brian Hampton <[email protected]> wrote: > I'm trying to figure out how to select an appropriate significance level, > e.g. the adjusted ratio p-value, for the protein abundance ratio for a > particular data set. In the 2003 Analytical Chem paper describing > ASAPRatio, it says that "certain p-values can be chosen as significant in > assessing protein abundance changes." And this is based on how well the > normal distribution (eq 1 in the paper) fits the overall data of unchanged > proteins. > > In the paper (http://tools.proteomecenter.org/publications/Li.ASAP.pdf) > they choose a p-value cutoff of <0.1 as their significance cutoff. Fig. 5 > shows the distribution of unique peptide ratios and a curve fit to the main > peak of peptides whose ratios do not change. And it shows a nice shoulder > of peptides with increased abundance ratios but I can't figure out how to > decide on a p-value cutoff for what is a significant abundance ratio for > the experiment. How is this done? > > Thanks in advance for your input. > > Brian Hampton > > -- > 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.
