How can the medianpolish used in RMA ensure that both alpha (probe affinity) and beta (expression abundance) larger than zero? Or, RMA occasionally gives out negative expression values? Thanks! Simon

There is no such constraint on signs in the algorithm itself. However, remember that the expression values returned from RMA are in log2 scale so negatives are not really negatives. That said, it is not common in my experience to ever see negative values (even in the log2 scale) being returned. If such a thing is happening for your data it might be indicative of some other problem. On Mon, 2005-05-30 at 16:34 -0500, Simon Lin wrote: > How can the medianpolish used in RMA ensure that > both > alpha (probe affinity) and beta (expression abundance) > larger than zero? > > Or, RMA occasionally gives out negative expression values? > > Thanks! > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad

Simon Lin wrote: > How can the medianpolish used in RMA ensure that > both > alpha (probe affinity) and beta (expression abundance) > larger than zero? > > Or, RMA occasionally gives out negative expression values? Medianpolish is run on log transformed values, so if by chance there were a bunch of data in the range (0 - 1) before taking logs, it is possible that some of the expression values could be negative. However, I have analyzed hundreds of chips and have yet to see a negative value, so I think the likelihood of such a thing happening is remote. Best, Jim > > Thanks! > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623