I was wondering what uncoloured rectangles signify in the image plots. Thanks Krys Dr Krystyna A Kelly (Krys) Department of Pathology University of Cambridge, Tennis Court Road, Cambridge CB2 1QP Tel: 01223 333331 and MRC Biostatistics Unit Institute of Public Health, Robinson Way, Cambridge CB2 0SR Tel: 01223 767408 Email: kak28 at cam.ac.uk

Dear Krys, > I was wondering what uncoloured rectangles signify in the image plots. Uncoloured rectangles occur when there is no data to plot in that particular region on the array surface. There are a few reasons why this might occur. 1. If the region only contains outliers and BeadScan has been configured to remove the outliers, then there will be no data to plot. 2. If the data is corrupt in that region (e.g. if log=TRUE and the region only contains NAs -> nothing sensible to plot). 3. Another possibility, which only occurs when an image plot of the residuals is made, is that the region only contains beads which haven't been decoded properly (ProbeID = 0). Bead types which have not been successfully decoded are not summarised, so won't have a residual, and are thus ignored for the image plot. Best wishes, Matt