Hi, I am unable to find answers to two queries based on a paper (*arrayQualityMetrics--a bioconductor package for quality assessment of microarray data*) and a book (*Bioconductor Case Studies*). Wonder if anybody could help: 1. I understand that a heatmap is a representation of distances between the arrays, where the median of the absolute values of the difference between each array-pair is considered as a measure of distance. That is, *Mxi *= *zi *+ *â**xi** *+ *å**xi* where *Mxi *and *Myi *represents the *M*-value of the *i*th probe on the *x* and *y* array. For *âxi *, which represents differential expression effects, it is said that the majority of its values are negligibly small (or close to zero). Why is it so ? Is this because median/mean gene may possibly be assumed to be not expressed !! Please let me know. 2. How to interpret a heatmap ? Let's say there is a heatmap of same framework as that of Fig. 3.2, page 30 of the book, *Bioconductor Case Studies* (http://tinyurl.com/2ervgpn). I understand that a heatmap provides the distance matrix entries (dxy), and in expectation, all the values of dxyare the same, namely 2-times the *å**xi*. However, what are the key elements in a figure such as Fig. 3.2 ? If the key elements are the tree-diagram on the top and the colour scale on the right, then how to interpret them in the sense that (depending on the diagram,) a set of one/more arrays can be declared as outlier array(s). I have tried but failed to find any explanation. Your reply (replies) would be very helpful. Kind regards, Chintanu [[alternative HTML version deleted]]