Dear Users,                  MAplot(affy) (ma.plot function), by default considers the pseudo-median reference chip. I would like to know how it is calculated ? if at probe level or probe set level what does the pseudo median reference signify. can any one suggest some reference on this. thank you , Sundar See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ [[alternative HTML version deleted]]

Hi Sundar, sundar Venkat wrote: > Dear Users, > MAplot(affy) (ma.plot function), by default considers the pseudo-median reference chip. > I would like to know how it is calculated ? if at probe level or probe set level what does the pseudo median reference signify. The MAplot() function takes an AffyBatch as input, so by definition the plot is at the probe level. It is calculated by extracting the probe data and running the rowMedians() function, which will give you a median value for each probe. If you want to peruse the function yourself, you can do so by showMethods("MAplot", includeDefs = TRUE) Best, Jim > > can any one suggest some reference on this. > > thank you , > Sundar > > > > See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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