What effects can be predicted with poor sample quality? How robust is the platform with questionable sample quality (such as FFPE samples)?
FAQ ID -2918

Poor quality samples tend to give higher Cts in all assays (mutation assays and gene copy number assays) and there are two possible consequences:

 (1) if using average Ct method for data analysis, even real mutations in poor quality samples will not be called, because the mutation locus Ct will be pushed to a high Ct region; (2) if using delta delta Ct method for data analysis, there will be a number of false positives in low quality samples.

We recommend using the average Ct value for gene copy number assays on the array to gauge the sample quality (or run the sample on a DNA QC plate before running samples on an array). For FFPE samples, we recommend the average Ct to be below 32 to allow sensitive detection of mutations. Samples that meet this criterion perform robustly on the arrays.