>Hi Everyone >I use custom designed chicken high-density multiplex one channel microarray (NimbleGen 12x135K). My usual >pipeline includes mostly oligo, arrayQualityMetrics, preprocessCore, genefilter, GeneSelector and limma. So >far I only worked with simple design, 2 conditions; control/treatment style. Now I have a dataset with >embryonic development timeline for male and female chicks. I still compare different timepoints using limma >but I want to do 2 way anova to identify interaction significant genes, ie genes where gender influences >development timeline. I looked at many packages and could not find 2 way anova, though I am sure it is there >somewhere. I tested package ABarray that seemed ideal for my me but after days of trying I contacted the >author to find out that expression sets (mine is coming from limma) can no longer be used by ABarray as the >package has not been updated for a while. Can anyone suggest a package (and an example code if possible) for >2 way anova? I am so tempted to go and do it in GeneSpring... >Thanks all >Dana Dana, The timecourse package is designed to handle temporal data across biological conditions and we've had good results from this package. I will add that we've compared expression between genders in temporal data and the most significant genes are sex-linked. Dennis Burian, Ph.D. FAA Functional Genomics Group 405-954-6087 dennis.burian at faa.gov