Hi to all, I've to deal with a dataset that has a huge amount of flagged as "bad" spots. My data are from peptide microarrays and the proportion of flags is around the 90% in each slide. Luckily I have a good set of samples (35 cases and 35 controls), but I'm not an expert with this kind of problem. Should I treat the flagged data as missing values and so try to impute new values instead the flagged "bad" spots ? I know the KNN imputation or the SVD imputation. What is normally done with the spots flagged as "bad" (-100, following GenePix criteria + additional criteria) in cDNA experiments ? Sorry if the question looks banal, but as I said I'm not an expert on this field. Any help is useful, also links regarding flagged data analysis... Thanks in advance, Davide -- Davide Valentini PhD - Biostatistician Department of Medical Epidemiology and Biostatistic Karolinska Institute Box 281 SE-171 77 Stockholm SWEDEN Tel: +46-8-524 82294 Fax: +46-8-31 4975