When using Control Samples Paired with Experimental Samples as the Sample Set(s) to Use for Subtraction, check this option to perform experimental minus control calculations targeted for interrogating loss of heterozygosity (or copy number count gain or loss).
Checking this box enables the Control Reference Value parameter field below. The value entered there is used as a filter for the control samples. The control adjustment (experimental - control) is performed only when the control sample has the value entered below (for example, numeric genotype or copy number count). Otherwise, a zero (0) is returned for both the experimental sample and control sample value.
For example, if you have paired sample genotypes for a tumor tissue sample and a normal tissue sample and want to find loci where genotypes have changed from heterozygous in the normal sample to homozygous in the control sample, you would specify a 1 in the field below. The resulting data set would contain 1 (or -1 if not using the absolute value of the difference) for every tumor tissue genotype that changed from 1 in the normal tissue sample to 0 or 2 in the tumor tissue. Every other value would be 0 or a missing value.
Note: Missing values in the output data set result only when the genotype or copy number count for the control sample is equal to the Control Reference Value, and a missing value is given for the genotype or copy number count for the paired experimental sample.
WARNING: Using this option with continuous measurement data (for example, copy number intensities) will likely return all zeros (0) in the output data set.
