Hi, I have three same sample running on the Affy test3 chip. I would like to check if the data is consistency. I run affyPLM package. I test results of RLE and NUSE. The results as follows: RLE(Pset,type ="stats") QCtest1.CEL QCtest2.CEL median 0.00000000 0.00000000 IQR 0.04745306 0.07492608 QCtest3.CEL median 0.00000000 IQR 0.07739142 > NUSE(Pset, type ="stats") QCtest1.CEL QCtest2.CEL median 1.00000000 1.00000000 IQR 0.02190403 0.01405276 QCtest3.CEL median 1.00000000 IQR 0.01762973 Attached is the image of RLE and NUSE box plot. In fact, the box plot confused me. Some box on the top of the median line. What is the problem? Any input is appropriated. Terry.