Figure 7

Other Examples of BioPNG Histogram Count File. (A) The BioPNG Histogram Count File can illustrate patterns in the frequency of different data values, another indicator of corrupt data. This example shows a periodic effect caused by lack of decimal values in higher intensity values that is not apparent in the lower intensity values. This is not necessarily a sign of data corruption, but may be related to rounding in the algorithm that converts DAT files to CEL files. (B) The BioPNG Pixel Count File can illustrate patterns in how the DAT to CEL conversion algorithm determines the number of pixels to use in the intensity calculation. Variations in this calculation are systematic and seem to correspond to very small differences in the orientation of the chip in the tray where it is read by the laser. Lighter pixels represent spots where more pixels being used in the calculation (and less being thrown out) while darker pixels represent fewer pixels bing used. Work is underway to determine if certain patterns are correlated to noisy, low-quality chip results. (These files have been cropped and brightened to make the patterns more visible in printed form.)