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

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