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.
