Hi David, What I am looking for is how to choose a ratio p-value *cutoff* that one can use to report which proteins are more likely to be differentially expressed vs more likely to be background. In the ASAPRatio publication they choose a p-value of <0.1 but I cannot figure out if this was arbitrarily chosen based on knowledge of the sample, or determined from some aspect of the quantitation data statistics.
Also, I want to thank everyone from the Seattle Proteome Center who came to Boston to teach the TPP course 2 weeks ago. I really learned a lot about the TPP and how to use it. It was an invaluable experience. Thanks! Brian Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 800 West Baltimore Street Rm 307 Baltimore MD 21201 V: 410-706-8207 F: 410-706-8234 On Wed, Sep 19, 2012 at 4:39 PM, David Shteynberg < [email protected]> wrote: > 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. > -- 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.
