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.
