Hi, I have a data set of 3 biological repeats. My proposed workflow for data pre-processing: background adjustment -> normalization( lowess normalization to a median array)-> Li and Wong's method of model-based calculation of expression index. Any thoughts on which method of background adjustment to use (RMA; MAS; Ideal mismatch) would be highly appreciated. Thank you in advance. Anjan -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]

Hi Anjan, On 9/28/2010 5:03 PM, ANJAN PURKAYASTHA wrote: > Hi, > I have a data set of 3 biological repeats. > My proposed workflow for data pre-processing: background adjustment -> > normalization( lowess normalization to a median array)-> Li and Wong's > method of model-based calculation of expression index. > Any thoughts on which method of background adjustment to use (RMA; MAS; > Ideal mismatch) would be highly appreciated. I'm not sure what you mean by '3 biological repeats'. Three per group? Three total samples? How many samples total do you have? Assuming you have few chips (3 or 6 or so), Li and Wong isn't going to work too well for you. If you look at the help page for this function you will see that the recommendation is to have at least 10 arrays. If you are sure you like Li and Wong's algorithm, you will likely be better served by using dChip. Best, Jim > Thank you in advance. > Anjan > -- 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