Hello, I have been processing Agilent long-oligo (60-mer) microarray data. After scanning the microarray slide, I used ScanAlyze to convert the image into numerical data. Then, I applied Total Intensity Normalization and LOWESS to normalize the data. However, the MA-plot after the normalization indicated that the data points at the higher A-value deviate from the M = 0 line. The whole plot looks like a flying bird with its beak pointing towards the lower edge of the plot. After examining the scanned image of the data, I found that most of these deviated data points were growing yellow. Thus, it should not affect the further analysis of this data, but I am curious to know if anyone has ever seen something like this. Is this typical for Agilent microarray data? Thank you. Shizuka