There is a fundamental difference between data collected in comprehensive two-dimensional gas chromatographic (GC ?? GC) separations and data collected by one-dimensional GC techniques (or heart-cut GC techniques). This difference can be ascribed to the fact that GC ?? GC generates multiple sub-peaks for each analyte, as opposed to other GC techniques that generate only a single chromatographic peak for each analyte. In order to calculate the total signal for the analyte, the most commonly used approach is to consider the cumulative area that results from the integration of each sub-peak. Alternately, the data may be considered using higher order techniques such as the generalized rank annihilation method (GRAM). Regardless of the approach, the potential errors are expected to be greater for trace analytes where the sub-peaks are close to the limit of detection (LOD). This error is also expected to be compounded with phase-induced error, a phenomenon foreign to the measurement of single peaks. Here these sources of error are investigated for the first time using both the traditional integration-based approach and GRAM analysis. The use of simulated data permits the sources of error to be controlled and independently evaluated in a manner not possible with real data. The results of this study show that the error introduced by the modulation process is at worst 1 for analyte signals with a base peak height of 10 ?? LOD and either approach to quantitation is used. Errors due to phase shifting are shown to be of greater concern, especially for trace analytes with only one or two visible sub-peaks. In this case, the error could be as great as 6.4 for symmetrical peaks when a conventional integration approach is used. This is contrasted by GRAM which provides a much more precise result, at worst 1.8 and 0.6 when the modulation ratio (MR) is 1.5 or 3.0, respectively for symmetrical peaks. The data show that for analyses demanding high precision, a MR of 3 should be targeted as a minimum, especially if multivariate techniques are to be used so as to maintain data density in the primary dimension. For rapid screening techniques where precision is not as critical lower MR values can be tolerated. When integration is used, if there are 4a??5 visible sub-peaks included for a symmetrical peak at MR = 3.0, the data will be reasonably free from phase-shift-induced errors or a negative bias. At MR = 1.5, at least 3 sub-peaks must be included for a symmetrical peak. The proposed guidelines should be equally relevant to LC ?? LC and other similar techniques.