There are a couple of things you can do. Using the siggenes package you can take your log ratios and calculate one-sample t-statistics, where you are testing to see if the mean of the ratios differs from zero. This is probably the easiest thing to do. If you want to convert your data back to log intensity values, you can then either use siggenes or multtest. In this case you would probably want to use a two-sample paired t-test because there is a clear dependence between the two samples hybridized to a given chip. It is simple to convert your M and A values back to log intensity values. A function to do so would look something like this: convert.back <- function(M, A){ G <- NULL R <- NULL for (i in 1:length(M)){ G[i] <- (2*A-M)/2 R[i] <- (2*A + M)/2 } return(cbind(R,G)) } 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 >>> Robert Cribbie <cribbie@criblab.yorku.ca> 11/12/03 02:13PM >>> I am a "newcomer" to the field of microarray analysis and I have run into a snag trying to analyze some cdna data. To determine if the same gene in two different groups is differentially expressed I assume that I am comparing the expression levels of the two groups after normalization. However, when I use bioconductor to normalize the data (e.g., maNorm) I only end up with matrices of log ratios (maM). How do I compare the expression levels of the two groups if I only have the log ratios (and not the normalized expression levels). Thanks for any help that you can provide. Rob. ********************************************************************** ****** Robert A. Cribbie Assistant Professor Associate Coordinator Department of Psychology Statistical Consulting Service York University Institute for Social Research Toronto, Ontario, Canada York University M3J 1P3 Phone: 416-736-5115 (x88615) E-Mail: cribbie@yorku.ca Fax: 416-736-5814 Website: http://www.psych.yorku.ca/cribbie _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor