Dear all, I have some basic statistical questions and which packages might provide tools to answer those. I am running R 2.0.1 + Bioconductor under Debian testing. I did have a look at the archives but did not find any satisfying answers (or I didn't search the right way) and since I have only a limited statistical background I need some pointers/help. 1. I have 4 sets of mice (wt vs treated) that have been hybridized as random pairs to a total of 8 oligo arrays (each pair twice as a dye swap pair). Each array is spotted in duplo. I would like to not only identify genes that are differentially expressed between the two experimental groups (wt and treated) but I also want to extract the effect of the treatment from the mouse individual effect of each mouse-pair(this effect could then be used as a factor in determining the required number of animals for a new experiment). I assume that each hybridisation will differ from the other pairs due to the mouse-(or patient-)effect. Is there an easy way to extract this information? Any hint to which package I should use or vignettes that discuss this issue would be greatly appreciated (if I know where to look for I usually get things running). 2. I do not have only on treatment but actually two treatments. The groups were hybridised in a loop design. I was told that I could only perform an ANOVA if I split the ratios (is this true?). I was also told this was dangerous business if I could not guarantee that the correlation between the individual green and red channels of each experimental group was "good" enough. My question is therefore, how can I check the correlation? Should I run a normalisation on the individual channels of each array or do I have to test the correlation on raw channel data (which differ quit a lot, hence the normalization, at least thats what I thought). What is a good correlation anyhow? Our Oligo-arrays are printed on home made slides, so quality is always an issue, where do I have to draw a line? And, if I have to work with ratios after all is there no other statistical approach to the loop design? I fear that these are very basic questions you probably get every now and then but I would greatly appreciate any help. Thanks, Anja -- Anja E. Schiel, Ph.D. Departments of General Internal Medicine and Human Genetics Leiden University Medical Center PO Box 9503 2300 RA Leiden The Netherlands tel: -31-(0)71-5276067 fax: -31-(0)71-5276075