[BioC] A doubt on Volcano Plot

[James W. MacDonald]

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