1. An in vitro method for determining a ratio of fetal to maternal DNA and a ploidy state of a set of chromosomes of interest in a mixed sample comprising DNA from a fetus and DNA from the mother of the fetus, the method comprising: obtaining genotypic data from the mixed sample for a set of single nucleotide polymorphisms (SNPs) on a set of chromosomes comprising at least one chromosome that is expected to be disomic and at least one chromosome whose ploidy state is to be determined, using a genetic measurement platform, by amplifying and measuring at least 500 SNP alleles from the mixed sample which is derived from maternal blood or maternal plasma and comprises free floating fetal and maternal DNA, wherein the amount of DNA measured at each allele at each SNP of the set of SNPs will depend on the number and type of alleles present at that SNP for the mother and the fetus and the overall concentrations of DNA present in the sample from the mother and the fetus; determining a mathematical characterization of the input/output characteristics of the genetic measurement platform using the measured genetic data from the chromosome expected to be disomic; creating, on a computer, a set of expected measurements for a possible set of inherited alleles for the set of SNPs for the mixed sample for different ploidy states at different ratios of fetal to maternal DNA in the mixed sample using the mathematical characterization; and determining on a computer, the ratio of fetal to maternal DNA and the ploidy state of the chromosome of interest in the mixed sample by comparing the genotypic measurements of the mixed sample to the set of expected measurements, wherein the ploidy determination is made with a computed confidence.