(1) Anova for 12 Affy yeast chips (Yg98) I'm going to try to explain the problem in a better way. I have the following experimental design : Fraction 1 Fraction 2 Medium A Fraction 3 * Medium B * 2 Reps - Fractions 1, 2 and 3 are three distinct subcellular mRNA populations ; - Medium A and B are two distinct culture medium ; - By Rep is meant a 'biological repetition'. That is cells harvested independantly from which the 3 Fractions are extracted. I have two sets of three Fractions in Medium A and two sets of three Fractions in Medium B. I am interested in finding - in a given medium - the distribution of each mRNA among the 3 Fractions. I thougth the data quite suited for ANOVA, at least as a first analytic step. The model would explain the log expression value by the sum of : - a constant term (maybe null actually) - a gene effect : approximately 6000 levels - a fraction effect : 3 levels - a medium effect : 2 levels - a rep effect : 2 levels for each medium - and possibly all two-order interactions. As wrote before, I couldn't apply directly 'lm' or 'aov' in R due to memory problems (the matrix to inverse being too large). Nor could I use Matlab Stat toolbox 'anovan' function which resulted in a disaster or the 'MANOVA' free matlab toolbox which is clearly specialised in cDNA array data. I am to try SAS 'proc anova' soon which should at least provide me average effects (that I admit are not so interesting by themselves). Before I calculate the whole thing myself, as a last solution, I wanted to make sure nobody had the idea of a particular tool to use directly or adapt easily. I looked rapidly at the 'Anova' function in the Genefilter package but it seems to use lm and to be limited to a one-way analysis hence I didn't find how to take advantage of it. (2) Problem fitting Li&Wong model with Affy 1.0 : I get almost the same problem wusing the cel.container mechanism (actually I didn't try it before because I thought I was to use a command called read.cel.container which in fact does not seem to exist) : > myfiles = c("xxx1.cel", "xxx2.cel",...) > lcel = read.container.celfile(filenames = myfiles > cdf = read.cdffile("Yg_s98.CDF") > eset = generateExprSet(lcel, cdf, method = "liwong", normalize = F) > eset = generateExprSet(lcel, cdf, method = "liwong") 9335 ids to go process... instancianting an exprSet... Error in data.matrix[, !phi.outliers] %*% phi[!phi.outliers] : non-conformable arguments > traceback() 4: which(cdf@name == i, arr.ind = TRUE) 3: locate.name(ids[id], cdf, type = "pm") 2: .local(x, cdf, method, ...) 1: generateExprSet(lcel, cdf, method = "liwong") Thank you. JS.