LabChip GX/GXII User Manual

Glossary of Terms 251Data FilteringBefore identification of peaks in the fluorescence data can proceed,the raw data must be smoothed to prevent the detection of signalnoise as peaks.To smooth the data, the LabChip GX software:1 Eliminates any narrow spikes from the data and replaces thespike with a local average of surrounding points.2 Applies baseline correction (if selected in the Assay Analysiswindow) to the data.• For the “Zero Baseline” option, a single value of baselineshift is determined by averaging over a 1 second region justbefore the Data Range Baseline time. This shift is subtractedfrom all of the data.• The “Baseline Subtraction” option uses a spline fit to thedata to determine a smooth baseline that is subtracted fromthe data. The percentage of data points used in the spline fitis specified by the Threshold value in the Assay Analysiswindow. The collection of points with the lowest variance upto this percentage is used for the spline fit.3 Smooths the data using a Savitzky-Golay filter using the FilterWidth and Polynomial Order specified in the Peak Find Tab ofthe Assay Analysis Window.DNA Assay AnalysisDNA samples contain two marker peaks outside the limits of theDNA fragment sizes the assay is designed to detect. The ladderscontain the same two marker peaks. The sample data is aligned tothe ladder data by matching the peak times of the two markers inthe sample data with the same two markers in the ladder data. Thesize of each sample peak is calculated by linear interpolationbetween the known ladder peak migration time and size using thepeak aligned migration time. The analysis settings can be changedto perform the interpolation using a local third order polynomial fit tothe time instead of the size relationship provided by the ladder.The concentration of the sample peaks is calculated using theknown area and concentration of the ladder peaks. The molarity ofeach sample peak is calculated using the sample concentration, theDNA fragment size (in base pairs) attributed to the peak, and theknown molecular weight of the DNA base pair.P/N 127170 Rev. 00 LabChip GX User Manual Caliper Life Sciences, Inc.