A method was proposed for estimating noise relative to signal in microarray data. A signal to noise index, SNI, was defined and used to measure the level of signal compared to the noise contained in two microarray data sets. Simulations were conducted to generate the quantitative relationship between the SNI and its measurement of relative noise. The method was applied to two well known microarray data sets. Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating relative noise in microarray data.