Dear Gordon, Excuse me for the last mail, I simply replied, I didn't realise that I was sending it to your personal email. I have also another problem with limma GUI- the Gene pix flag weighting. In my gpr file I have flag bad (-100), flag not found(-50) and unflagged (0), when I use spot quality weighting and some steps later I choose only 2 of the spot types (mir and mirPlus) I get the error message: "asMatrixWeights (weights, dim(M)), weigths of unexpected shape" I checked the mailing list and saw that you recommended someone else witht the same problem to check the size of the objects. I tried to do this inserting in the R console "dim(weights)" immedialtely after choosing the spot qualities in the limma Gui and it tells "NULL", which doesn't look fine to me. But I'm not sure if performing the setting of the flags on the GuInterface creates an object "weight" in R console? Since I am using limma GUI, I do not understand where I am introducing the error, since the only information I give is the gal and gpr file- they contain the same number of features. The sum of the spottypes that he is reading from the spottype file is correct (corresponds to the number of features in gal and gpr file,= 5632) Read CV 40_900750_110908.gpr Read CV41_complete1_900740_120908.gpr Read CV42_complete1_900760_120908.gpr Read CV43_upsidedown1_9000740_250908.gpr Read CV44_complete1_900750_300908.gpr Matching patterns for: ID Name Found 2904 mir Found 152 miRPlus Found 8 positivectrl Found 40 positivectrl2 Found 28 negativectrl Found 316 spikes Found 156 virus Found 68 virus1 Found 8 virus2 Found 12 virus3 Found 68 virus4 Found 8 virus5 Found 1616 noname Found 88 empty Found 160 Hy3 Setting attributes: values Color > weights (dim) NULL If something is wrong with the dimensions of the object I load I guess this could also explain the problems that I have with the replictaes? THank you very much for your time and your support, Christine -- Dr. Christine Völlenkle, Ph.D. Research Laboratories-Molecular Cardiology I.R.C.C.S. Policlinico San Donato Via R. Morandi, 30 20097 S. Donato M.se (MI) Italy Phone: +39 02 52774 683 (lab) +39 02 52774 533 (office) Fax: +39 02 52774 666 email: christine.voellenkle@gmail.com [[alternative HTML version deleted]]