Dear BioC Users, When Affycomp gives a MA plot, there are both negative and positive infinities (in black ink) as plotting symbols on the plot. I noticed that they are also present on the example MA plots in the Cope, et.al (2005) paper. I have been unable to find an explanation of what these mean, and would appreciate it if someone could tell me what they represent. On a related note, is placement of these positive and negative infinities related to the performance of the method? Thanks, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035

Hi Monnie, McGee, Monnie wrote: > Dear BioC Users, > > When Affycomp gives a MA plot, there are both negative and positive > infinities (in black ink) as plotting symbols on the plot. I noticed > that they are also present on the example MA plots in the Cope, et.al > (2005) paper. I have been unable to find an explanation of what > these mean, and would appreciate it if someone could tell me what > they represent. The Affy latin square dataset includes samples where no probe was spiked in (hence the concentration is 0 pMol). So the infinite fold changes result when the unspiked sample is in the denominator or numerator (+inf and -inf, respectively). On a related note, is placement of these positive > and negative infinities related to the performance of the method? I don't know about this one. Presumably there is some 'native' transcript for each gene (or at least some noise component for each probe), so the fold change shouldn't really be infinite. However, I don't think there is a good way to know how much transcript already existed in the sample to try and figure out where the infinite fold change points should really end up. Best, Jim > > Thanks, Monnie > > Monnie McGee, Ph.D. Assistant Professor Department of Statistical > Science Southern Methodist University Ph: 214-768-2462 Fax: > 214-768-4035 > > > -------------------------------------------------------------------- ---- > > > _______________________________________________ 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.