I quite like the idea of the positive border elements plots in affyQCReport. However, I have a few suggestions for improvements and would like to know what people think, and also how to go about achieving it. 1) I think the boxplots should use log2 intensities rather than raw intensities. 2) The way that +ve/-ve border elements are identified in the code essentially takes all the spots around the perimeter of the array - PM and MM. Positive and Negative border elements for each side of the array are identify from the border elements (which contain PM and MM probes) which are greater than 1.2 or less than 0.8 times the mean respectively. Since, the distribution of intensities for a particular border contains both PM and MM probes, there will be a bi-modal distribution to complicate things. It seems to me, that it might be better to have a PM border elements and MM border elements plotted on a log2 scale. Therefore, my question is: How do I obtain the PM and MM probe intensities separately from an AffyBatch object for the first and last rows and columns of an array? i.e. I want 8 vectors containing intensities for the PM and MM probes for each of the four sides of an array. Thanks for any help/comments, Nathan ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222 ------------------------------------------------------------- [[alternative HTML version deleted]]