Hi, I'm trying to use GeneCluster to analyze our GeneChip data normalized with RMA. However, there is another normalization option in GeneCluster: Normalize to Mean ____ and Variance ____ The results I got with or without this step are quite different, even though the data has been treated with RMA. What does this normalization process do? Should I do this step + RMA or should I just rely on RMA? Thanks for your help. Mingqian Huang

Assuming that GeneCluster makes a 'heatmap' like Eisen's software, you will probably have to normalize the data using GeneCluster, for two reasons. 1.) In order for the data to be visualized as being up or down regulated, they have to be distributed around zero. Down regulated genes will have negative expression values and up regulated genes will have positive values. 2.) If GeneCluster is similar to Eisen's cluster, the range for the colors is (-3, 3), where -3 is as dark a green as you will get and 3 is as bright a red. Any values outside this range will not be distinguishable. Therefore, data are usually mean (or median) centered (e.g., mean=0), and the variance adjusted to 1. However, I am making a BIG assumption that GeneCluster is similar to Eisen's Cluster. If I am wrong, my apologies in advance. ;-D 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 >>> "Huang, Mingqian " <mhuang1@partners.org> 10/15/03 12:10PM >>> Hi, I'm trying to use GeneCluster to analyze our GeneChip data normalized with RMA. However, there is another normalization option in GeneCluster: Normalize to Mean ____ and Variance ____ The results I got with or without this step are quite different, even though the data has been treated with RMA. What does this normalization process do? Should I do this step + RMA or should I just rely on RMA? Thanks for your help. Mingqian Huang _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor