Hello All, I was trying to construct a volcano plot from protein abundance ratio. So far my understanding goes each ratio( or log_ratio) can have only one Z score and hence one corresponding P-value to the Z-score. But in volcano plots there are multiple P values(along Y axis) for a given ratio(or log_ratio). How does this happen? Do they pool replicate data with slightly different mean and std_dev so that Z score and P-value are different for a given ratio. I've posted a related question in the R-Help list but yet to get any response: https://stat.ethz.ch/pipermail/r-help/attachments/20110119/fe1a253b/at tachment.pl http://img402.imageshack.us/i/volcanoi.jpg/ [[alternative HTML version deleted]]

On 1/20/2011 10:07 AM, B Enn wrote: > Hello All, > I was trying to construct a volcano plot from protein abundance ratio. > So far my understanding goes each ratio( or log_ratio) can have only one > Z score and hence one corresponding P-value to the Z-score. > But in volcano plots there are multiple P values(along Y axis) for a given > ratio(or log_ratio). How does this happen? Do they pool replicate data with > slightly different mean and std_dev so that Z score and P-value are > different for > a given ratio. No, each point on a volcano plot represents the fold change and p-value for a single gene. When you have thousands of measurements (from e.g., a microarray), it is likely that many will have very similar fold change values. Best, Jim > > I've posted a related question in the R-Help list but yet to get any > response: > > https://stat.ethz.ch/pipermail/r-help/attachments/20110119/fe1a253b/ attachment.pl > > http://img402.imageshack.us/i/volcanoi.jpg/ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues