The effect of underlying copy number variations on gene expression differences between peritoneal and primary tumors. A. Greater than 2000 genes were used for the analysis. When gene expression data is analyzed by groups of patients containing either amplification (amp), or deletion (del) CNV, the gene expression differences are more significant (SeparatedByCNV). When patients are all analyzed together (NoSeparation), without separating them based on underlying CNVs, the gene expression differences are significantly decreased. As expected, the average gene expression differences between primary and peritoneum in genes outside of CNVs (noCNVs) is near zero. Gene expression data from patients without CNVs do not change. B. For each gene in a patient's primary/metastatic pair, the primary tumor expression value was subtracted from the metastatic expression value. The paired gene expression differences for all genes in each patient were then subjected to principal components analysis in Partek.