Dear list, I have a very basic question regarding Poisson noise or shot noise with respect to differential expression analysis of digital gene expression data. As an example, if one source of RNA was made into 7 identical RNA-Seq libraries and then sequenced on 7 individual lanes, when comparing the sequence data we would still expect differences between the gene counts due to shot noise. Using the rpois() function I generated some data that follows a Poisson distribution and checked the data distribution in terms of standard deviations. In contrast to the 68-95-99.7 rule for the normal distribution, I observed percentages of 73-96-99.6. So in my digital gene expression example above, if I calculated the mean across the 7 technical replicates for one particular gene, I can expect that the counts for each respective library should lie within one or two standard deviations of the mean. Is this what the Poisson or shot noise is referring to? Many thanks, -- Dave