Hi I am using Affy package in R and using M vs A plots (in two chip comparisons only) to identify differentially expressed genes. How do I locate a gene of interest on an M vs A plot? Regards. Anthony -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au

I don't know how you would identify the genes from the plot, but it is simple to identify them from the data. Lets say your M and A values are in a matrix or data.frame (we'll call it df): M A Gene1 3.1 5 Gene2 0.1 8 Gene3 1.1 12 Gene4 -0.5 4 <snip> Do something like filter <- abs(df[,1]) > 1 # For two-fold differential expression top.genes <- df[filter,] # Will give you those genes that exceed your cutoff. If you really want to know which gene is what point in your plot, you can do something like text(top.genes[,2], top.genes[,1], labels=row.names(df), cex=0.7) HTH, Jim 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 >>> Anthony Bosco <anthonyb@ichr.uwa.edu.au> 11/05/03 02:34AM >>> Hi I am using Affy package in R and using M vs A plots (in two chip comparisons only) to identify differentially expressed genes. How do I locate a gene of interest on an M vs A plot? Regards. Anthony -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor