Hi This question counts for most of the microarray packages... When calculating the average differential expression for replicate spots, do you take an averge of the log2(ratio)'s, or the log2 of the average ratio? (they come up with different numbers) Which one and why? Thanks Mick

Hi Mick, michael watson (IAH-C) wrote: > Hi > > This question counts for most of the microarray packages... > > When calculating the average differential expression for replicate > spots, do you take an averge of the log2(ratio)'s, or the log2 of the > average ratio? (they come up with different numbers) > > Which one and why? The mean of the log2(ratios). The main reason for doing so is to make the data look more like they come from a Normal distribution. On the natural scale the down-regulated genes will have a range from (0,1] and the up-regulated genes will have a range from [1, inf), so the distribution of these data will have a strong right skew. If you take logs then the range will be (-inf, 0], [0, inf) for down and up-regulated genes, respectively. Much of the analyses that we perform with these data assume that each datum is a Normal variate (for instance, the t-test), so you have to take logs first to make the data look more Normal. Another reason is to minimize/eliminate any dependence of the variance on the expression level. In other words, we would like the variability of the data to be relatively consistent regardless of the spot intensity. Taking logs tends to help in this respect as well. HTH, Jim > > Thanks > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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