LabChip GX/GXII User Manual

Data Analysis 69Upper and Lower Marker Peaks for DNA AssaysFor each DNA sample, the upper and lower marker peaks areassigned first and then the data is aligned so that the well markersmatch the ladder markers in time, allowing the size andconcentration of the sample peaks to be determined.For DNA assays, the first peak is assigned to be the lower markerand is then offset to match the lower marker in the ladder. Theupper marker is then assigned to the last peak in the sample well orto the peak nearest the ladder’s upper marker. The Upper Markerand Lower Marker are aligned to the ladder markers by resamplingthe well data in a linear stretch or compression using a point-topointfit.If the sample marker peaks are either more than twice as far apartor less than half as far apart as the ladder markers, they areassumed to be the wrong peaks, and analysis of the well stops,producing the error Marker peaks not detected.In DNA assays, the height of marker peaks is assay dependant.Ladder peaks are analyzed to calculate a marker peak thresholdthat is used to locate the marker peaks in the sample wells. If themarker peaks found using this calculated method fail to align withthose of a sample, the LabChip GX software will use the minimumpeak height threshold setting instead (if this value is lower than thevalue for the marker peak). For example, the calculated thresholdmight be too high to find the sample's markers if they happen to bevery small for some reason. Either no markers will be found or thewrong peaks will be assumed to be markers and these may notalign with the ladder markers. Consequently, the software attemptsto use the minimum peak height threshold that, if it is set lowenough, will catch the real markers, allowing the sample to align.If you get unexpected peaks in the ladder analysis or the markershave been set incorrectly, you can manually exclude peaks or set apeak to be used as a marker.NOTES• Excluding a peak or manually setting a peak to be an upper orlower marker for a DNA assay can cause errors with analysis.• You can move the boundary between the Peak Table and theGraph view up or down to increase or decrease the size of thePeak Table, making it possible to see all of the results at once.P/N 127170 Rev. 00 LabChip GX User Manual Caliper Life Sciences, Inc.