Hello. I've just started using the marray package for processing a set of spotted oligo arrays. The arrays, when intensities or log ratios are plotted against probe number, show a clear pattern of rising/falling values with a periodicity equal to the grid block size (~3600 spots). I can see a similar periodicity in the printTip boxplots generated with marray. Running printTipLoess smoothes out the boxplot nicely (and the MA plot also looks much nicer), but, surprisingly, when I export the normalized values and plot them against position, the grid block periodicity is little changed. I've tried different span values for the printTipLoess as well as trying with or without scaling (e.g. printTipMAD), but nothing I do seems to have much effect on this data artifact. Does anyone have any suggestions? Thanks. -- Gene Cutler Research Investigator Bioinformatics Amgen SF