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


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