Hi Susanne, On 2/3/2012 10:27 AM, Susanne Gerber wrote: > Dear James, > thank you so much for the very fast and detailed response. > I will start answering your questions: > >> I assume that by 'two independent time series' you mean that these experiments were conducted at different times, perhaps in different labs, etc? > The first experiment was performed half a year earlier but within the > same lab and by the same experimenter. Ugh. <shoots self=""> > >> The second problem is due to the fact that you never hybridized MU and WT samples on the same chip, >> which has introduced another untestable and unquantifiable 'chip' effect. > Well, this is actually the problem I am struggling with. > >> You could hypothetically do a single channel analysis with these data, >> but any comparison between MU and WT would include both biological and technical variability, >> and you won't be able to say how much of either. >> Again, you can assume that the technical variability is small, but you won't really be able to say for sure if this assumption is true. > I think I have to do so, since these data are the only dataset I have. > I am not an experimenter and the lab where the data originally came > from can not perform these new experiments (the cells are not > available any more, project ran out last year, no money, no staff...). > Thats what I meant by saying "it is also not possible to repeat the > experiment and produce a direct comparison." > Sorry for being so imprecise. :) > > The maanova package is great and I already used it, however I still do > not know how to perform this single channel analysis you were talking > about with my two-colour data. > What would be the best way (or is there already an existing package > for this) to treat the data and to extract the information ? Yes, look at the limma User's Guide, starting on p. 52. Best, Jim > > Thanks again so much for your help > Best regards, > Susanne > > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues